Magnetic Needle Alignment Tool? The 139 Latest Answer

needle

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function

description

Global Needleman-Wunsch alignment of two sequences

Needle reads two input sequences and writes their optimal global sequence alignment to the file. It uses the Needleman-Wunsch alignment algorithm to find the optimal alignment (including gaps) of two sequences over their entire length. The algorithm uses a dynamic programming method to ensure that the alignment is optimal by examining all possible alignments and choosing the best one. A scoring matrix is ​​read containing scores for each possible residue or nucleotide match. Needle finds the alignment with the maximum possible score, where the score of an alignment is equal to the sum of the matches from the score matrix, minus the penalties resulting from opening and widening gaps in the aligned sequences. The substitution matrix and the gap opening and extension penalties are specified by the user.

algorithm

The Needleman-Wunsch algorithm is a member of the class of algorithms that can compute the best score and alignment of two sequences in order of mn steps, where n and m are the sequence lengths. These dynamic programming algorithms were first developed by Needleman and Wunsch for comparing protein sequences, although similar methods were developed independently in the late 1960s and early 1970s for use in the fields of language processing and computer science.

An important problem is the treatment of gaps, i. H. Spaces inserted to optimize alignment score. For each gap opened, a penalty is deducted from the score (the penalty for opening the gap) and a penalty is deducted from the score for the total number of gap spaces multiplied by cost (the penalty for widening the gap). Typically, the cost of widening a gap is 5 to 10 times lower than the cost of opening a gap.

The penalty for a gap of n positions is calculated using the following formula:

Gap Opening Penalty + (n – 1) * Gap Extension Penalty

In a global Needleman-Wunsch alignment, the entire length of each sequence is aligned. The sequences may partially overlap, or one sequence may be completely internally aligned with the other. There is no penalty for the hanging ends of the overlap. In bioinformatics it is usually reasonable to assume that the sequences are incomplete and there should be no penalty for not aligning the missing bases.

purpose of use

Here is an example session with

% Needle tsw:hba_human tsw:hbb_human Needleman request global alignment of two sequences Gap Opening Penalty [10.0]: Gap Extension Penalty [0.5]: Output Alignment [hba_human.needle]:

Browse to the input files for this example

Browse to the output files for this example

command line arguments

Needleman request global alignment of two sequences Version: EMBOSS:6.6.0.0 Default (Mandatory) Qualifiers: [-aequence] sequence sequence filename and optional format or reference (input USA) [-bsequence] seqall sequence(s) filename and optional format or reference (Input USA) -gapopen float [10.0 for each sequence] The gap open penalty is the score taken when a gap occurs. The best value depends on the choice of comparison matrix. The default assumes you are using the EBLOSUM62 matrix for protein sequences and the EDNAFULL matrix for nucleotide sequences. (Float from 1.0 to 100.0) -gapextend float [0.5 for each sequence] The gap extension penalty is added to the default gap penalty for each base or remainder in the gap. Gaps that long will be penalized. Typically, you’ll expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is when one or both sequences are single reads with possible sequencing errors, in which case you would expect many single base gaps. You can achieve this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. (Float number from 0.0 to 10.0) [-outfile] align [*.needle] Output alignment filename (default -aformat srspair) Additional (optional) qualifiers: -datafile matrixf [EBLOSUM62 for protein, EDNAFULL for DNA] This is the scoring matrix file used when comparing sequences. By default, this is the “EBLOSUM62” file (for proteins) or the “EDNAFULL” file (for nucleic sequences). These files are located in the “data” directory of the EMBOSS installation. -endweight boolean [N] Applies gap penalties at the end. -endopen float [10.0 for each sequence] The end gap open penalty is the score that is deducted when an end gap occurs. The best value depends on the choice of comparison matrix. The default assumes you are using the EBLOSUM62 matrix for protein sequences and the EDNAFULL matrix for nucleotide sequences. (Float from 1.0 to 100.0) -endextend float [0.5 for each sequence] The penalty for extending the ending gap is added to the penalty for the ending gap for each base or remainder in the ending gap. End gaps that long will be penalized. (Floating point from 0.0 to 10.0) Advanced (unsolicited) qualifiers: -[no]brief boolean [Y] Brief identity and similarity Related qualifiers: “-aequence” Associated qualifiers -begin1 integer Begin of sequence to use -send1 integer End of sequence to use -sreverse1 boolean reverse (if DNA) -sask1 boolean asks for start/end/reverse -snucleotide1 boolean sequence is nucleotide -sprotein1 boolean sequence is protein -slower1 boolean lower case -supper1 boolean upper case – scircular1 boolean sequence is circular – squick1 boolean Read ID and sequence only -sformat1 string input sequence format -iquery1 string enter query fields or id list -ioffset1 integer enter start position offset -sdbname1 string database name -sid1 string entry name -ufo1 string UFO functions – fformat1 string features format -fopenfile1 string features filename ” -bsequence” related qualifiers -begin2 integer Beginning of each sequence to use -send2 integer End of each sequence to use -sreverse2 boolean reverse (if DNA) -sask2 boolean Ask for start/end/return -snucleotide2 boolean sequence is nucleotide -sprotein2 boolean sequence is protein -slower2 boolean Lowercase -supper2 boolean Uppercase -scircular2 boolean Sequence is circular -squick2 boolean Read ID and sequence only -sformat2 string Input sequence format -iquery2 string Enter query fields or ID list -ioffset2 integer Enter start position offset -sdbname2 string database name -sid2 string entry name -ufo2 string UFO functions -fformat2 string function format – fopenfile2 string properties filename qualifiers associated with “-outfile” -aformat3 string alignment format -aextension3 string filename extension -adirectory3 string output directory -aname3 string base filename -awidth3 integer out directionwidth -aaccshow3 boolean Show handle in header -adesshow3 boolean Show description in header -ausashow3 boolean Show full USA in alignment -aglobal3 boolean Show full s sequence in alignment Common specifiers: -auto boolean Disable prompts -stdout boolean Write first file to standard output -filter boolean Read first file from standard input, write first file to standard output -options boolean Get default and additional values ​​-debug boolean Write debug output to program.dbg -verbose boolean Report some/complete command line options -help boolean Report command line options and exit. For more information on mapped and general qualifiers, see -help -verbose -warning boolean Report warnings -error boolean Report errors -fatal boolean Report fatal errors -die boolean Report dying program messages -version boolean Report version number and exit

Qualifier Type Description Allowed Values ​​Default Default (Required) Qualifiers [-sequence]

(Parameter 1) sequence sequence filename and optional format or reference (input USA) human-readable sequence required [-bsequence]

(Parameter 2) seqall sequence(s) filename and optional format or reference (input USA) Human-readable sequence(s) Required -gapopen float The gap opening penalty is the score taken when a gap is created. The best value depends on the choice of comparison matrix. The default assumes you are using the EBLOSUM62 matrix for protein sequences and the EDNAFULL matrix for nucleotide sequences. Float from 1.0 to 100.0 10.0 for each sequence -gapextend float The gap extension penalty is added to the default gap penalty for each base or remainder in the gap. Gaps that long will be penalized. Typically, you’ll expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is when one or both sequences are single reads with possible sequencing errors, in which case you would expect many single base gaps. You can achieve this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. Floating point number from 0.0 to 10.0 0.5 for each sequence [-outfile]

(Parameter 3) align output alignment filename (default -aformat srspair) <*>.needle Additional (optional) qualifiers -datafile matrixf This is the scoring matrix file used when comparing sequences. By default, this is the “EBLOSUM62” file (for proteins) or the “EDNAFULL” file (for nucleic sequences). These files are located in the “data” directory of the EMBOSS installation. Comparison matrix file in EMBOSS datapath EBLOSUM62 for protein

EDNAFULL for DNA -endweight boolean Apply end gap penalties. boolean yes/no no -endopen float The end gap open penalty is the score taken away when an end gap is created. The best value depends on the choice of comparison matrix. The default assumes you are using the EBLOSUM62 matrix for protein sequences and the EDNAFULL matrix for nucleotide sequences. Float from 1.0 to 100.0 10.0 for each sequence -enextend float The penalty for extending the tail gap is added to the tail gap penalty for each base or remainder in the tail gap. End gaps that long will be penalized. Floating point number from 0.0 to 10.0 0.5 for each sequence Advanced (unprompted) qualifiers -[no]brief boolean Brief identity and similarity boolean Yes/No Yes Associated qualifiers “-aequence” Associated sequence qualifiers -begin1

-begin_aequence integer Begin of sequence to use Any integer value 0 -send1

-send_aequence integer End of sequence to use Any integer value 0 -sreverse1

-sreverse_asequence boolean reverse (if DNA) boolean yes/no N -sask1

-sask_asequence boolean Ask for start/end/reverse boolean yes/no N -snucleotide1

-snucleotide_asequence boolean sequence is nucleotide boolean yes/no N -sprotein1

-sprotein_asequence boolean sequence is protein boolean yes/no N -slower1

-slower_aequence boolean Make lowercase boolean yes/no N -supper1

-supper_aequence boolean Make uppercase boolean yes/no N -scircular1

-scircular_aequence boolean sequence is circular boolean yes/no N -squick1

-squick_aequence boolean Read ID and sequence only boolean yes/no N -sformat1

-sformat_aequence string Input sequence format Any string -iquery1

-iquery_aequence string input query fields or id list any string -ioffset1

-ioffset_a sequence integer Enter the offset of the start position Any integer value 0 -sdbname1

-sdbname_asequence string database name any string -sid1

-sid_aequence string entry name any string -ufo1

-ufo_aequence string UFO functions any string -fformat1

-fformat_asequence string features format any string -fopenfile1

-fopenfile_aequence string features filename any string “-bsequence” associated seqall qualifiers -begin2

-begin_bsequence integer Begin of each sequence to use Any integer value 0 -send2

-send_bsequence integer End of any sequence to use Any integer value 0 -sreverse2

-sreverse_bsequence boolean reverse (if DNA) boolean yes/no N -sask2

-sask_bsequence boolean Ask for start/end/reverse boolean yes/no N -snucleotide2

-snucleotide_bsequence boolean sequence is nucleotide boolean yes/no N -sprotein2

-sprotein_bsequence boolean sequence is protein boolean yes/no N -slower2

-slower_bsequence boolean Make lowercase boolean yes/no N -supper2

-supper_bsequence boolean Make uppercase boolean yes/no N -scircular2

-scircular_bsequence boolean sequence is circular boolean yes/no N -squick2

-squick_bsequence boolean Read ID and sequence only boolean yes/no N -sformat2

-sformat_bsequence string Input sequence format Any string -iquery2

-iquery_bsequence string input query fields or id list any string -ioffset2

-ioffset_bsequence integer Enter the offset of the starting position Any integer value 0 -sdbname2

-sdbname_bsequence string database name any string -sid2

-sid_bsequence string entry name any string -ufo2

-ufo_bsequence string UFO functions any string -fformat2

-fformat_bsequence string features format any string -fopenfile2

-fopenfile_bsequence string feature filename any string alignment qualifiers associated with “-outfile” -aformat3

-aformat_outfile string alignment format any string srspair -aextension3

-aextension_outfile string filename extension any string -adirectory3

-adirectory_outfile string output directory any string -aname3

-aname_outfile string Base file name Any string -awidth3

-awidth_outfile integer alignment width Any integer value 0 -aaccshow3

-aaccshow_outfile boolean Show accession number in header boolean yes/no N -adesshow3

-adesshow_outfile boolean Display description in header boolean yes/no N -ausashow3

-ausashow_outfile boolean Show full USA aligned boolean yes/no N -aglobal3

-aglobal_outfile boolean Show full sequence in alignment boolean yes/no Y General qualifiers -auto boolean Disable prompts boolean yes/no N -stdout boolean Write first file to stdout boolean yes/no N -filter boolean Read first file from standard input write first file to standard output boolean yes/no N -options boolean query for standard and additional values ​​boolean yes/no N -debug boolean write debug output to program.dbg boolean yes/no N -verbose boolean Report some/full command line options boolean yes/no Y -help boolean Report command line options and exit. For more information on related and general qualifiers, see -help -verbose boolean yes/no N -warning boolean Report warnings boolean yes/no Y -error boolean Report errors boolean yes/no Y -fatal boolean Report fatal errors boolean value yes/no Y -die boolean Report dying program messages boolean yes/no Y -version boolean Report version number and exit boolean yes/no N

input file format

reads in two nucleotide or protein sequences. The second input can be more than one sequence to align with the first input sequence.

The input is a standard EMBOSS sequence query (aka “USA”).

Major sequence database sources defined by default in EMBOSS installations include srs:embl, srs:uniprot, and ensembl

Data can also be read from the sequence output in any supported format written by an EMBOSS or third-party application.

The input format can be specified using the -sformat xxx command line qualifier, where “xxx” is replaced with the name of the required format. The available format names are: gff (gff3), gff2, embl (em), genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw), dasgff and debug.

See: http://emboss.sf.net/docs/themes/SequenceFormats.html for more information on sequence formats.

Input files for application example

‘tsw:hba_human’ is a sequence entry in the example protein database ‘tsw’

Database entry: tsw:hba_human

ID HBA_HUMAN verified; 142AA. AC P69905; P01922; Q1HDT5; Q3MIF5; Q53F97; Q96KF1; Q9NYR7; Q9UCM0; DT 07/21/1986, integrated in UniProtKB/Swiss-Prot. DT 23 JAN 2007, sequence version 2. DT 13 JUN. 2012, entry version 108. DE RecName: Full = hemoglobin subunit alpha; DE AltName: Full=Alpha Globin; EN AltName: Full=hemoglobin alpha chain; GN name=HBA1; GN and GN name=HBA2; OS Homo sapiens (human). OC Eukaryota; metazoa; chordates; craniata; vertebrates; euteleostomy; OC mammals; eutheria; Euarchontoglires; primates; haplorrhini; OC Catarrhini; hominids; Homo. OX NCBI_TaxID=9606; RN[1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA1). RX-MEDLINE=81088339; PubMed=7448866; DOI=10.1016/0092-8674(80)90347-5; RA Michelson A.M., Orkin S.H.; RT “The 3′ untranslated regions of the duplicated human alpha globin RT genes are unexpectedly different.”; RL Cell 22:371-377 (1980). RN[2] RP NUCLEOTIDE SEQUENCE [mRNA] (HBA2). RX-MEDLINE=80137531; PubMed=6244294; RA Wilson J.T., Wilson LB., Reddy V.B., Cavallesco C., Ghosh P.K., RA Deriel J.K., Forget BG., Weissman SM.; RT “Nucleotide sequence of the coding portion of human alpha-globin RT messenger RNA.”; RL J. Biol. Chem. 255:2807-2815 (1980). RN[3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (HBA2). RX-MEDLINE=81175088; PubMed=6452630; DOI=10.1073/pnas.77.12.7054; RA Lieber S.A., Goossens M.J., Kan Y.W.; RT “Cloning and complete nucleotide sequence of the human 5′-alpha globin RT gene.”; RL proc. national Academic Science. USA 77:7054-7058 (1980). RN[4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX PubMed=6946451; DOI=10.1073/pnas.78.8.5041; RA Orkin S.H., Goff S.C., Hechtman R.L.; RT “Mutation in an intervening splice junction in humans.”; RL proc. national Academic Science. USA 78:5041-5045 (1981). RN[5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] AND VARIANT LYS-32. RX-MEDLINE=21303311; PubMed=11410421; RA Zhao Y, Xu X; RT “Alpha2(CD31 AGG–>AAG, Arg–>Lys) causes non-deletive alpha RT thalassemia in a Chinese family with HbH disease.”; [Part of this file deleted for brevity] FT /FTId=VAR_002841. FT VARIATION 132 132 S -> P (on Questembert; very unstable; FT causes alpha thalassemia). FT /FTId=VAR_002843. FT-VARIANT 134 134 S -> R (in Val de Marne; O(2)-affinity FT upwards). FT /FTId=VAR_002844. FT-VARIANT 136 136 V -> E (in Pavie). FT /FTId=VAR_002845. FT VARIANT 137 137 L -> M (in Chicago). FT /FTId=VAR_002846. FT VARIATION 137 137 L -> P (in Bibba; unstable; causes alpha FT thalassemia). FT /FTId=VAR_002847. FT VARIANT 137 137 L -> R (in Toyama). FT /FTId=VAR_035242. FT VARIANT 139 139 S -> P (in Attleboro; O(2) affinity above). FT /FTId=VAR_002848. FT VARIATION 140 140 K -> E (in Hanamaki; O(2) affinity high). FT /FTId=VAR_002849. FT VARIANT 140 140 K -> T (in Tokoname; O(2) affinity high). FT /FTId=VAR_002850. FT VARIANT 141 141 Y -> H (in Rouen/Ethiopia; O(2) affinity FT up). FT /FTId=VAR_002851. FT VARIANT 142 142 R -> C (in Nunobiki; O(2) affinity above). FT /FTId=VAR_002852. FT VARIANT 142 142 R -> H (in Suresnes; O(2) affinity high). FT /FTId=VAR_002854. FT VARIANT 142 142 R -> L (in Legnano; O(2) affinity above). FT /FTId=VAR_002853. FT VARIANT 142 142 R -> P (in Singapore). FT /FTId=VAR_002855. FT CONFLICT 10 10 N -> H (in Ref. 13; BAD97112). FT HELIX 5 16 FT HELIX 17 21 FT HELIX 22 36 FT HELIX 38 43 FT HELIX 54 72 FT HELIX 74 76 FT HELIX 77 80 FT HELIX 82 90 FT HELIX 97 113 FT TURN 115 117 FT HELIX 120 117 FT TURN 115 117 FT HELIX 120 117 FT HELIX 13 7 FT HELIX 120 117 FT HELIX 138 QUENCE 138 142AA; 15258MW; 15E13666573BBBAE CRC64; MVLSPADKTN VKAAWGKVGA HAGEYGAEAL ERMFLSFPTT KTYFPHFDLS HGSAQVKGHG KKVADALTNA VAHVDDMPNA LSALSDLHAH KLRVDPVNFK LLSHCLLVTL AAHLPAEFTP AVHASLDKFL ASVSTVLTSK YR //

Database entry: tsw:hbb_human

ID HBB_HUMAN checked; 147AA. AC P68871; A4GX73; B2ZUE0; P02023; Q13852; Q14481; Q14510; Q45KT0; AC Q549N7; Q6FI08; Q6R7N2; Q8IZI1; Q9BX96; Q9UCD6; Q9UCP8; Q9UCP9; DT 07/21/1986, integrated in UniProtKB/Swiss-Prot. DT 23 JAN 2007, sequence version 2. DT 13 JUN. 2012, entry version 108. DE RecName: Full = hemoglobin subunit beta; DE AltName: Full=Beta Globin; EN AltName: Full=hemoglobin beta chain; DE Contains: DE RecName: Full=LVV-hemorphin-7; GN name=HBB; OS Homo sapiens (human). OC Eukaryota; metazoa; chordates; craniata; vertebrates; euteleostomy; OC mammals; eutheria; Euarchontoglires; primates; haplorrhini; OC Catarrhini; hominids; Homo. OX NCBI_TaxID=9606; RN[1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX-MEDLINE=77126403; PubMed=1019344; RA Marotta C, Forget B, Cohen-Solal M, Weissman SM; RT “Nucleotide sequence analysis of coding and non-coding regions of human RT beta-globin mRNA.”; RL Prog. Mol. biol. 19:165-175 (1976). RN[2] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RX-MEDLINE=81064667; PubMed=6254664; DOI=10.1016/0092-8674(80)90428-6; RA Lawn RM, Efstratiadis A, O’Connell C, Maniatis T; RT “The nucleotide sequence of the human beta-globin gene.”; RL Cell 21:647-651 (1980). RN[3] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] AND VARIANT LYS-7. RX PubMed=16175509; DOI=10.1086/491748; RA Wood ET, Stover DA, Slatkin M, Nachman M.W., Hammer M.F.; RT “The beta-globin recombination hotspot reduces the effects of strong RT selection around HbC, a recent mutation that confers RT resistance to malaria.”; RL Am. J.Hum. genetics 77:637-642 (2005). RN[4] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RA Lu L, Hu ZH, Du CS, Fu YS; RT “Human beta-globin gene DNA sequence isolated from a healthy RT Chinese.”; RL Submitted (JUN-1997) to the EMBL/GenBank/DDBJ databases. RN[5] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] AND VARIANT ARG-113. Cabeda J.M., RA Correia C., Estevinho A., Cardoso C., Amorim ML., Cleto E. RA, Vale L., Coimbra E., Pinho L., Justica B.; RT “Unexpected patterns of globin mutations in thalassemia patients from RT north of Portugal.”; [Part of this file deleted for brevity] FT VARIANT 141 141 A -> V (in Puttelange; polycythemia; O(2) FT affinity high). FT /FTId=VAR_003082. FT VARIANT 142 142 L -> R (in Olmsted; unstable). FT /FTId=VAR_003083. FT VARIANT 143 143 A -> D (in Ohio; O(2) affinity above). FT /FTId=VAR_003084. FT VARIANT 144 144 H -> D (at Rancho Mirage). FT /FTId=VAR_003085. FT VARIANT 144 144 H -> P (in Syracuse; O(2) affinity above). FT /FTId=VAR_003087. FT-VARIANT 144 144 H -> Q (in Little Rock; O(2)-affinity FT upwards). FT /FTId=VAR_003086. FT VARIANT 144 144 H -> R (in Abruzzo; O(2) upward affinity). FT /FTId=VAR_003088. FT VARIANT 145 145 K -> E (in Mito; O(2) affinity above). FT /FTId=VAR_003089. FT VARIANT 146 146 Y -> C (in Rainier; O(2) affinity above). FT /FTId=VAR_003090. FT VARIANT 146 146 Y -> H (in Bethesda; O(2) affinity high). FT /FTId=VAR_003091. FT VARIANT 147 147 H -> D (in Hiroshima; O(2) affinity above). FT /FTId=VAR_003092. FT VARIANT 147 147 H -> L (in Cowtown; O(2) affinity above). FT /FTId=VAR_003093. FT VARIANT 147 147 H -> P (in York; O(2) affinity above). FT /FTId=VAR_003094. FT VARIATION 147 147 H -> Q (in Kodaira; O(2) affinity up). FT /FTId=VAR_003095. FT CONFLICT 26 26 Missing (in ref. 15; ACD39349). FT CONFLICT 42 42 F -> L (in Ref. 13; AAR96398). FT HELIX 6 16 FT TURN 21 23 FT HELIX 24 35 FT HELIX 37 42 FT HELIX 44 46 FT HELIX 52 57 FT HELIX 59 77 FT TURN 78 80 FT HELIX 82 94 FT TURN 95 97 FT HELIX 102 4 2FT 2.2 119 FT HELIX HELIX 144 146 SQ SEQUENCE 147 AA; 15998MW; A31F6D621C6556A1 CRC64; MVHLTPEEKS AVTALWGKVN VDEVGGEALG RLLVVYPWTQ RFFESFGDLS TPDAVMGNPK VKAHGKKVLG AFSDGLAHLD NLKGTFATLS ELHCDKLHVD PENFRLLGNV LVCVLAHHFG KEFTPPVQAA YQKVVAGVAN ALAHKYH //

output file format

The output is a standard EMBOSS alignment file.

The results can be output in one of several styles by using the -aformat xxx command line qualifier, where “xxx” is replaced with the name of the required format. Some of the alignment formats can handle an unlimited number of sequences, while others are only suitable for pairs of sequences.

The multiple alignment format names available are: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs.

The available format names for pairwise alignment are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair

See: http://emboss.sf.net/docs/themes/AlignFormats.html for more information on alignment formats.

Output files for application example

File: hba_human.needle

##################################### # Program: Nadel # Round Date: Mon 15 Jul 2013 12 :00:00 # command line: needle # [-aequence] tsw:hba_human # [-bsequence] tsw:hbb_human # Align_format: srspair # Report_file: hba_human.needle ############## ## ########################========================= ============== # # Aligned_sequences: 2 # 1: HBA_HUMAN # 2: HBB_HUMAN # Matrix: EBLOSUM62 # Gap_penalty: 10.0 # Extend_penalty: 0.5 # # Length: 149 # Identity: 65 /149 (43.6%) # Similarity: 90/149 (60.4%) # Gaps: 9/149 (6.0%) # Score: 292.5 # # #=========== ====== ====================== HBA_HUMAN 1MV-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-D48 || |:|.:|:.|.|.|||| :..|.|.|||.|:.:.:|.|:.:|..| | HBB_HUMAN 1 MVHLTPEEKSAVTALWGKV–NVDEVGGEALGRLLVVYPWTQRFFESFGD 48 HBA_HUMAN 49 LS—–HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLR 93 || .|:.:||.|||||..|.::.:||:|::….:.||:||..||. HBB_HUMAN 49 LSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLH 98 HBA_HUMAN 94 VDPVNFKLLSHCLLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR 142 |||.||:||.:.|:..||.|…||||.|.|:..|.:|.|:. .|..||. HBB_HUMAN 99 VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH 147 #—————————————————- #—– ———————————-

The identity: is the percentage of identical matches between the two sequences over the reported aligned region (including any gaps in length).

The Similarity: is the percentage of matches between the two sequences over the reported aligned region (including any gaps in length).

file

For protein sequences, EBLOSUM62 is used for the substitution matrix. EDNAFULL is used for the nucleotide sequence. Others can be specified.

EMBOSS data files are distributed with the application and stored in the default EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

Run the following to view the available EMBOSS data files:

% Emboss Data -showall

To load one of the data files (e.g. “Exxx.dat”) into your current directory so that you can examine or modify it, run:

% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project-specific files can be placed in the current directory or, for cleaner directory listings, in a subdirectory called “.embossdata”. Files for all EMBOSS runs can be placed in the user’s home directory or again in a subdirectory called “.embossdata”.

The directories are searched in the following order:

. (your current directory)

.embossdata (under your current directory)

~/ (your home directory)

~/.embossdata

Remarks

references

Needleman, S.B. and Wunsch, CD. (1970) J. Mol. Chem. 1997, 1996, 1997. biol. 48, 443-453. Kruskal, J.B. (1983) A review of sequence comparison In D. Sankoff and J.B. Kruskal, (eds.), Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison, pp. 1-44 Addison Wesley.

warnings

is a true implementation of the Needleman-Wunsch algorithm, thus generating a complete path matrix. It therefore cannot be used with genome-sized sequences unless you have a lot of memory and time. It’s about aligning two sequences over their entire length. This works best with closely related sequences. Using a needle to align very distantly related sequences will yield a result, but much of the alignment may have little or no biological significance.

A true Needleman-Wunsch implementation like Needle requires memory proportional to the product of the sequence lengths. Therefore, for two sequences of length 10,000,000 and 1,000, it requires storage proportional to 10,000,000,000 characters. Two arrays of this size will be produced, one with ints and one with floats, so multiply that number by 8 to get the memory usage in bytes. This does not include other overhead costs. Verwenden Sie daher Wasser und Nadel nur für die genaue Ausrichtung einigermaßen kurzer Sequenzen.

Wenn Ihnen der Speicherplatz ausgeht, versuchen Sie es stattdessen mit der Trage.

Diagnosefehlermeldungen

Nicht erfasste Ausnahme Assertion schlug bei ajmem.c:xxx fehl

Wahrscheinlich bedeutet, dass Ihnen der Speicher ausgegangen ist. Versuchen Sie in diesem Fall, eine Trage zu verwenden.

Exit-Status

Bekannte Fehler

Programmname Beschreibung est2genome Alignment von EST-Sequenzen an genomischer DNA-Sequenz needleall Viele-zu-viele paarweise Alignments von zwei Sequenzsätzen Stretcher Needleman-Wunsch Rapid Global Alignment von zwei Sequenzen

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Wenn Sie eine Ausrichtung wünschen, die die gesamte Länge beider Sequenzen abdeckt, verwenden Sie eine Nadel.

Wenn Sie versuchen, den besten Ähnlichkeitsbereich zwischen zwei Sequenzen zu finden, verwenden Sie Wasser.

stretcher ist ein besser geeignetes Programm, um globale Alignments sehr langer Sequenzen zu finden.

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Alan BleasbyEuropean Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

Bitte melden Sie alle Fehler dem EMBOSS-Fehlerteam (emboss-bug © emboss.open-bio.org) und nicht dem ursprünglichen Autor.

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Abgeschlossen am 8. Juli 1999.

Geändert am 26. Juli 1999 – Bewertung optimiert.

Geändert am 22. Oktober 2000 – %ID- und %Ähnlichkeitswerte hinzugefügt.

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Dieses Programm soll von jedem und allem verwendet werden, von naiven Benutzern bis hin zu eingebetteten Skripten. No

In ferromagnetic materials, smaller groups of atoms combine into areas called domains, where all the electrons have the same magnetic orientation. That’s why you can magnetize them. See how it works in this tutorial.

Electrons are tiny little magnets. They have a north and a south pole and rotate around an axis. This rotation results in a very small but extremely significant magnetic field. Each electron has one of two possible orientations for its axis.

In most materials, the magnetic orientation of one electron cancels the orientation of another. The situation is different with iron and other ferromagnetic substances (ferrum means iron in Latin). Their atomic structure results in smaller groups of atoms grouping together into areas called domains, where all of the electrons have the same magnetic orientation. Below is an interactive animation that shows you how these domains respond to an external magnetic field.

In the ferromagnetic material pictured above, the domains are randomly oriented (the figure shows how this phenomenon works, not the actual size or shape of the domains). Normally invisible magnetic field lines, shown in red, emanate from the poles of the bar magnet. Use the Magnet Position slider to move the magnet closer to the ferromagnetic material so that it interacts with the field lines. If you repeat the process, you will find that the domains gradually align – with the field of the bar magnet and with each other.

When you’re done, the ferromagnetic material itself has become a permanent magnet, a dipole with north-south opposite poles. A permanent magnet is nothing more than a ferromagnetic object with all domains oriented in the same direction.

There are only four elements in the world that are ferromagnetic at room temperature and can be permanently magnetized: iron, nickel, cobalt and gadolinium. (A fifth element, dysprosium, becomes ferromagnetic at low temperatures.)

Ferromagnets remain magnetized after exposure to an external magnetic field, sometimes for millions of years. This tendency to retain magnetism is called hysteresis.

Early human travelers used a variety of methods to avoid getting lost on their journeys. For terrestrial travel, they often used plants or other landmarks. That didn’t work at sea, however, where sailors instead relied on objects in the sky, including the sun, moon, and North Star, to guide their path. Of course, when clouds obscured these bodies, boats could easily get lost. The invention of the magnetic compass, believed to have been developed independently in China and Europe in the 11th or 12th centuries, made navigation both by sea and by land safer and much more accurate.

Experiment with the compass in this tutorial to see how it responds to magnetic fields. To move the horseshoe magnet to a new location, click and drag it. To see how a compass behaves when there is no magnet nearby to affect it, click the Hide Magnet button. You can make it reappear by clicking the Show Magnet button. Note that when the magnet is absent the compass needle points north, but when the magnet is present the needle points to the magnet. This is because the compass needle is magnetized and mounted so that it can move in response to magnetic fields. When the horseshoe magnet is in place, the north end of the needle (colored red) is attracted to its magnetic field and orients itself to point at the object. The closer the magnet is to the compass, the stronger the effect. Even with the magnet removed, the compass is still affected by magnetic forces – those associated with the earth. These forces usually cause the compass needle to point north (unless another magnet interferes) and make the device useful for navigation.

No one knows for sure what creates Earth’s magnetic field, but one of the most common explanations involves turbulent activity and currents in the planet’s molten iron core. The field is known to vary with time and even reverse periodically. So compasses, if they had existed at different times in the distant past, would not have pointed north but south, like compasses in future ages.

In fact, even the compasses currently in use do not generally point to true true north, since the Earth’s magnetic field is not exactly parallel to the globe’s north-south axis (although it is quite close). The difference between true north and magnetic north is called declination, and this value varies by location on the planet. Some modern compasses are designed to take declination into account and give a significantly better indication of direction.

15.4 The Compass (ESAEN)

A compass is an instrument used to determine the direction of a magnetic field. A compass consists of a small metal needle that is itself magnetized and is free to rotate in any direction. Therefore, in the presence of a magnetic field, the needle can orient itself in the same direction as the field.

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Magnetite, a magnetized form of iron oxide, orients itself north-south when allowed to spin freely in water by hanging it from a string or float. Lodestone was therefore used as an early navigational compass.

Compasses are mainly used in navigation to find direction on earth. This works because the Earth itself has a magnetic field similar to that of a bar magnet (see image below). The compass needle follows the direction of the earth’s magnetic field and points from north to south. Once you know where north is, you can figure out any other direction. A photo of a compass is shown on the right.

Some animals can detect magnetic fields, which helps them orient and navigate. Animals capable of doing this include pigeons, bees, monarch butterflies, sea turtles, and certain fish.

A compass

Photo by Alex on Flickr

The Earth’s Magnetic Field (ESAEO) The image below shows a representation of the Earth’s magnetic field, which closely resembles the magnetic field of a giant bar magnet like the one in the image to the right. The earth has two magnetic poles, a north and a south pole, just like a bar magnet. Besides the magnetic poles, the earth also has two geographic poles. The two geographic poles are the points on the earth’s surface where the line of the earth’s axis of rotation meets the earth’s surface. To illustrate this, you could take any round fruit (lemon, orange, etc.) and poke a pencil through the middle so it comes out the other side. Rotate the pencil, the pencil is the axis of rotation and the geographic poles are where the pencil enters and exits the fruit. We call the geographic North Pole true north. The Earth’s magnetic field has been measured very accurately, and scientists have found that the magnetic poles do not exactly correspond to the geographic poles. So the earth has two north poles and two south poles: geographic poles and magnetic poles. The direction of the earth’s magnetic field changes roughly every \(\text{200,000}\) years! You can think of it like a bar magnet whose north and south poles periodically switch sides. The reason for this is not yet fully understood. Earth’s magnetic field is thought to be caused by flowing liquid metals in the planet’s outer core, causing electric currents and a magnetic field. In the picture you can see that the direction of magnetic north and true north are not the same. The geographic north pole is approximately \(\text{11,5}\)\(\text{°}\) away from the direction of magnetic north (which a compass will point). However, the magnetic poles are constantly shifting slightly. Another interesting thing is that if we imagine the earth as a large bar magnet and we know that magnetic field lines always point north to south, the compass tells us that what we call the magnetic north pole is actually the south is the pole of the bar magnet!

Phenomena related to the Earth’s Magnetic Field (ESAEP) The importance of the magnetic field for life on Earth The Earth’s magnetic field is very important for humans and other animals on Earth because it protects us from being bombarded (hit ) to be emitted by the sun. The stream of charged particles (mainly positively charged protons and negatively charged electrons) coming from the sun is called the solar wind. When these particles get close to the earth, they are deflected by the earth’s magnetic field and are unable to rain down to the surface, where they can harm living organisms. Astronauts in space are at risk of being irradiated by the solar wind because they are outside the zones where the charged particles are trapped. Visualization of the magnetosphere The area above the earth’s atmosphere where charged particles are influenced by the earth’s magnetic field is called the magnetosphere. Relatively often, in addition to the usual solar wind, the Sun can eject a large bubble of matter (protons and electrons) from its outer atmosphere with its own magnetic field. Sometimes these bubbles travel to Earth, where their magnetic fields can combine with the Earth’s magnetic field. When this happens, a huge amount of energy is released into the Earth’s magnetosphere, causing a geomagnetic storm. These storms cause rapid changes in the Earth’s magnetosphere, which in turn can affect electrical and magnetic systems on Earth such as power grids, cell phone networks, and other electronic systems. Aurorae (pronounced Or-roar-ee) Another effect caused by Earth’s magnetic field is the spectacular Northern and Southern Lights, also known as the Aurora Borealis and Aurora Australis, respectively. When charged particles from the solar wind reach Earth’s magnetosphere, they spiral along the magnetic field lines toward the north and south poles. When they collide with particles in Earth’s atmosphere, they can cause red or green lights that span much of the sky, called an aurora. Aurora borealis photographed in Alaska Aurora australis photographed from space Because this only happens near the North and South Poles, we cannot see the Aurora Borealis of South Africa. However, people living in the high northern latitudes of Canada, Sweden and Finland, for example, often see the Northern Lights. Simulation: VPfkg

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The information below is taken from “Electricity and Magnetism: Berkeley Physics Course”, Vol. 2, 2nd Ed., by Edward M. Purcell.

We now understand that the magnetism of materials is derived from the movement of electrons within atoms. Electrons spin and effectively become rotating spheres of charge. That means they have a magnetic moment. In the diagrams above, the arrows indicate the direction of angular momentum. The magnetic moments point in the opposite direction. The intrinsic magnetic moment of an electron is 9284.764e-27 J. In most atoms, the electrons pair up and spin in opposite directions, and their magnetic moments then cancel. Some atoms have an odd number of electrons, meaning one is unpaired and its magnetic moment is not canceled. This type of atom is called “paramagnetic”. The magnetic moments in paramagnetic substances align themselves in an external field. However, thermal motion tends to disrupt the ordered arrangement of these freely pivoting magnetic moments; hence paramagnetism increases as temperature decreases.

In ferromagnetic, or what is commonly referred to as magnetic, materials, it is energetically favorable when the spins of neighboring atoms are parallel. This is due to the quantum mechanics of ferromagnetic atoms, and as a result areas form where magnetic moments line up in the same direction called domains. In an unmagnetized piece of iron, these magnetic domains point in random directions and cancel out, and there is no significant magnetic field. Magnetization causes magnetic domains to spread out in favorable directions and grow larger, creating a magnetic field. For example, when an external magnetic field is applied, the moments that are parallel to the field have lower energy than those that are not, making them energetically favorable. As a result, favorable domains grow because atoms at the boundaries take the preferred direction. The shift in domain structure causes the ferromagnetic material to develop a magnetic field.

The iron crystal structure is cubic as shown on the left. These cubic axes are the easiest axes of magnetization, which means that atoms will preferentially align in this direction. This is an important property of ferromagnetic materials because it prevents atoms from vibrating freely. In order to align in another of the preferred axes, the atoms would have to pass through less favorable positions. Because of this, permanent magnets largely retain the magnetization imparted to them.

Molecular Currents

Ampere’s model is surprisingly close to the truth. After all, there are no circular molecular currents, but the rotating electrons act like current loops. These “currents” actually want to flow in the same direction because each current loop is a magnetic dipole that will align in the same direction as a nearby dipole. Ampere thought that the currents inside cancel to result in a current flowing along the outside because the sides of the circular currents cancel adjacent sides until only the outer shell remains, as in this diagram from Gibson’s student notebook . In fact, the magnetic moments of the electrons cancel when they point in different directions. All magnetic moments add up to create the magnetic field, they are not reduced to a shell. Nor did Ampere know how the magnetization “started” these currents. We now know that the electrons have always rotated and always have a magnetic moment. It’s simply a matter of aligning these spins to create an overall magnetic effect. Ultimately, he is correct in his assumption that magnetic phenomena are the product of electricity, since all these ferromagnetic materials obtain their magnetic properties from the movement of charges at the atomic level.

As for the deflection of the galvanometer needle, the galvanometer coil generates a magnetic field as follows:

An external magnetic field exerts a torque on a magnetic dipole (e.g. the magnetic galvanometer needle) equal to the cross product of the magnetic moment and the magnetic field. Thus, the magnetic field within the coil and around the needle exerts a torque on the needle.

The black lines in the left diagram represent the coil’s magnetic field, while the green rectangle is the magnetic needle, with its poles marked and its magnetic moment pointing from S to N. If you take the cross product of the magnet moment and field vectors, the resulting torque vector shows out the side as in the right diagram. Thus, the magnetic field exerts a counterclockwise torque on the needle, causing it to rotate and align itself with the coil’s magnetic field. Because of this, the galvanometer needle deflects when current is passed through its coil.