infoalign Wiki The master copies of EMBOSS documentation are available at http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki. Please help by correcting and extending the Wiki pages. Function Display basic information about a multiple sequence alignment Description infoalign displays on screen basic information about sequences in an input multiple sequence alignment. This includes the sequences' USA, name, two measures of length, counts of gaps, and numbers of identical, similar and different residues or bases in this sequence when compared to a reference sequence, together with a simple statistic of the % change between the reference sequence and this sequence. Any combination of these records is easily selected or unselected for display. The same information may be written to an output file which (optionally) may be formatted in an HTML table. The reference sequence is the one against which all the other sequences are compared using a specified substitution matrix. It is either the calculated consensus sequence of the alignment (the default) or it can be one of the set of aligned sequences, specified by either the ordinal number of that sequence in the input file, or by name. There are various options to control how the consensus is calculated. Algorithm The set of aligned sequences is read in. If the reference sequence is the consensus sequence (this is the default) then this is calculated. If the reference sequence is specified as an ordinal number, then the sequences are counted (from 1) until the reference sequence is identified. If the reference sequence is specified by its name then the names of the sequences are compared to the specified name until the reference sequence is identified. Foreach sequence: Find the position of the first residue or base which is not a gap character. Find the position of the last residue or base which is not a gap character. Foreach position from the first non-gap character to the last non-gap character: if the position is a gap character, then increment the 'GapLen' count if this character is the start of a new gap, increment the 'Gaps' count else the character at this position of the sequence and in the reference sequence are now compared. if the sequence character and the reference character are identical (apart from case) then increment the 'Ident' count else if the similarity matrix score for the two characters is > 0 (i.e. if they are similar) then increment the 'Similar' count else increment the 'Different' count The 'SeqLen' length of the sequence is the number of non-gap characters in the sequence (i.e. 'Ident' + 'Similar' + 'Different') The 'AlignLen' length of the sequence is the length from the first non-gap character to the last non-gap character. (i.e. the number of bases or residues of the sequence plus the number of gap characters internal to the sequence.) The '%Change' value for the sequence is calculated as: ('AlignLen' - 'Ident') * 100 / 'AlignLen' Usage Here is a sample session with infoalign % infoalign globins.msf Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the input files for this example Go to the output files for this example Example 2 This example doesn't display the USA of the sequence: % infoalign globins.msf -nousa Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 3 Display only the name and sequence length of a sequence: % infoalign globins.msf -only -name -seqlength Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 4 Display only the name, number of gap characters and differences to the consensus sequence: % infoalign globins.msf -only -name -gapcount -diffcount Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 5 Display the name and number of gaps within a sequence: % infoalign globins.msf -only -name -gaps Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 6 Display information formatted with HTML: % infoalign globins.msf -html Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 7 Use the first sequence as the reference sequence to compare to: % infoalign globins.msf -refseq 1 Display basic information about a multiple sequence alignment Output file [globins.infoalign]: Go to the output files for this example Example 8 % infoalign -auto @eclac.list -out test.out Go to the input files for this example Go to the output files for this example Example 9 % infoalign -auto tembl:v00296 -out test.out Go to the input files for this example Go to the output files for this example Command line arguments Display basic information about a multiple sequence alignment Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqset The sequence alignment to be displayed. [-outfile] outfile [*.infoalign] If you enter the name of a file here then this program will write the sequence details into that file. Additional (Optional) qualifiers: -matrix matrix [EBLOSUM62 for protein, EDNAFULL for DNA] This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. -refseq string [0] If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence. The reference sequence is the one against which all the other sequences are compared. If this is set to 0 then the consensus sequence will be used as the reference sequence. By default the consensus sequence is used as the reference sequence. (Any string) -html boolean [N] Format output as an HTML table Advanced (Unprompted) qualifiers: -plurality float [50.0] Set a cut-off for the % of positive scoring matches below which there is no consensus. The default plurality is taken as 50% of the total weight of all the sequences in the alignment. (Number from 0.000 to 100.000) -identity float [0.0] Provides the facility of setting the required number of identities at a position for it to give a consensus. Therefore, if this is set to 100% only columns of identities contribute to the consensus. (Number from 0.000 to 100.000) -only boolean [N] This is a way of shortening the command line if you only want a few things to be displayed. Instead of specifying: '-nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight' to get only the sequence length output, you can specify '-only -seqlength' -heading boolean [@(!$(only))] Display column headings -usa boolean [@(!$(only))] Display the USA of the sequence -name boolean [@(!$(only))] Display 'name' column -seqlength boolean [@(!$(only))] Display 'seqlength' column -alignlength boolean [@(!$(only))] Display 'alignlength' column -gaps boolean [@(!$(only))] Display number of gaps -gapcount boolean [@(!$(only))] Display number of gap positions -idcount boolean [@(!$(only))] Display number of identical positions -simcount boolean [@(!$(only))] Display number of similar positions -diffcount boolean [@(!$(only))] Display number of different positions -change boolean [@(!$(only))] Display % number of changed positions -weight boolean [@(!$(only))] Display 'weight' column -description boolean [@(!$(only))] Display 'description' column Associated qualifiers: "-sequence" associated qualifiers -sbegin1 integer Start of each sequence to be used -send1 integer End of each sequence to be used -sreverse1 boolean Reverse (if DNA) -sask1 boolean Ask for begin/end/reverse -snucleotide1 boolean Sequence is nucleotide -sprotein1 boolean Sequence is protein -slower1 boolean Make lower case -supper1 boolean Make upper case -scircular1 boolean Sequence is circular -squick1 boolean Read id and sequence only -sformat1 string Input sequence format -iquery1 string Input query fields or ID list -ioffset1 integer Input start position offset -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-outfile" associated qualifiers -odirectory2 string Output directory General qualifiers: -auto boolean Turn off 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 Prompt for standard and additional values -debug boolean Write debug output to program.dbg -verbose boolean Report some/full command line options -help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -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 Input file format infoalign reads a normal multiple sequence alignment file, as produced by a alignment program. Input files for usage example File: globins.msf !!AA_MULTIPLE_ALIGNMENT 1.0 ../data/globins.msf MSF: 164 Type: P 25/06/01 CompCheck: 4278 .. Name: HBB_HUMAN Len: 164 Check: 6914 Weight: 0.61 Name: HBB_HORSE Len: 164 Check: 6007 Weight: 0.65 Name: HBA_HUMAN Len: 164 Check: 3921 Weight: 0.65 Name: HBA_HORSE Len: 164 Check: 4770 Weight: 0.83 Name: MYG_PHYCA Len: 164 Check: 7930 Weight: 1.00 Name: GLB5_PETMA Len: 164 Check: 1857 Weight: 0.91 Name: LGB2_LUPLU Len: 164 Check: 2879 Weight: 0.43 // 1 50 HBB_HUMAN ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR HBB_HORSE ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR HBA_HUMAN ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS HBA_HORSE ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG MYG_PHYCA ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD 51 100 HBB_HUMAN FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE HBB_HORSE FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE HBA_HUMAN FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD HBA_HORSE FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD MYG_PHYCA KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN 101 150 HBB_HUMAN LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA HBB_HORSE LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA HBA_HUMAN LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS HBA_HORSE LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS MYG_PHYCA SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA 151 164 HBB_HUMAN NALAHKYH~~~~~~ HBB_HORSE NALAHKYH~~~~~~ HBA_HUMAN TVLTSKYR~~~~~~ HBA_HORSE TVLTSKYR~~~~~~ MYG_PHYCA KDIAAKYKELGYQG GLB5_PETMA Y~~~~~~~~~~~~~ LGB2_LUPLU IVIKKEMNDAA~~~ Input files for usage example 8 File: eclac.list #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 Input files for usage example 9 'tembl:v00296' is a sequence entry in the example nucleic acid database 'tembl' Database entry: tembl:v00296 ID V00296; SV 1; linear; genomic DNA; STD; PRO; 3078 BP. XX AC V00296; XX DT 13-JUL-1983 (Rel. 03, Created) DT 18-APR-2005 (Rel. 83, Last updated, Version 5) XX DE E. coli gene lacZ coding for beta-galactosidase (EC 3.2.1.23). XX KW galactosidase. XX OS Escherichia coli OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. XX RN [1] RP 1-3078 RX PUBMED; 6313347. RA Kalnins A., Otto K., Ruether U., Mueller-Hill B.; RT "Sequence of the lacZ gene of Escherichia coli"; RL EMBO J. 2(4):593-597(1983). XX RN [2] RX PUBMED; 3038536. RA Zell R., Fritz H.J.; RT "DNA mismatch-repair in Escherichia coli counteracting the hydrolytic RT deamination of 5-methyl-cytosine residues"; RL EMBO J. 6(6):1809-1815(1987). XX CC Data kindly reviewed (18-MAY-1983) by U. Ruether XX FH Key Location/Qualifiers FH FT source 1..3078 FT /organism="Escherichia coli" FT /mol_type="genomic DNA" FT /db_xref="taxon:562" FT CDS <1..3072 FT /transl_table=11 FT /note="galactosidase" FT /db_xref="GOA:P00722" FT /db_xref="InterPro:IPR004199" FT /db_xref="InterPro:IPR006101" FT /db_xref="InterPro:IPR006102" FT /db_xref="InterPro:IPR006103" FT /db_xref="InterPro:IPR006104" FT /db_xref="InterPro:IPR008979" FT /db_xref="InterPro:IPR011013" FT /db_xref="InterPro:IPR013781" FT /db_xref="InterPro:IPR013812" [Part of this file has been deleted for brevity] gaggcccgca ccgatcgccc ttcccaacag ttgcgcagcc tgaatggcga atggcgcttt 180 gcctggtttc cggcaccaga agcggtgccg gaaagctggc tggagtgcga tcttcctgag 240 gccgatactg tcgtcgtccc ctcaaactgg cagatgcacg gttacgatgc gcccatctac 300 accaacgtaa cctatcccat tacggtcaat ccgccgtttg ttcccacgga gaatccgacg 360 ggttgttact cgctcacatt taatgttgat gaaagctggc tacaggaagg ccagacgcga 420 attatttttg atggcgttaa ctcggcgttt catctgtggt gcaacgggcg ctgggtcggt 480 tacggccagg acagtcgttt gccgtctgaa tttgacctga gcgcattttt acgcgccgga 540 gaaaaccgcc tcgcggtgat ggtgctgcgt tggagtgacg gcagttatct ggaagatcag 600 gatatgtggc ggatgagcgg cattttccgt gacgtctcgt tgctgcataa accgactaca 660 caaatcagcg atttccatgt tgccactcgc tttaatgatg atttcagccg cgctgtactg 720 gaggctgaag ttcagatgtg cggcgagttg cgtgactacc tacgggtaac agtttcttta 780 tggcagggtg aaacgcaggt cgccagcggc accgcgcctt tcggcggtga aattatcgat 840 gagcgtggtg gttatgccga tcgcgtcaca ctacgtctga acgtcgaaaa cccgaaactg 900 tggagcgccg aaatcccgaa tctctatcgt gcggtggttg aactgcacac cgccgacggc 960 acgctgattg aagcagaagc ctgcgatgtc ggtttccgcg aggtgcggat tgaaaatggt 1020 ctgctgctgc tgaacggcaa gccgttgctg attcgaggcg ttaaccgtca cgagcatcat 1080 cctctgcatg gtcaggtcat ggatgagcag acgatggtgc aggatatcct gctgatgaag 1140 cagaacaact ttaacgccgt gcgctgttcg cattatccga accatccgct gtggtacacg 1200 ctgtgcgacc gctacggcct gtatgtggtg gatgaagcca atattgaaac ccacggcatg 1260 gtgccaatga atcgtctgac cgatgatccg cgctggctac cggcgatgag cgaacgcgta 1320 acgcgaatgg tgcagcgcga tcgtaatcac ccgagtgtga tcatctggtc gctggggaat 1380 gaatcaggcc acggcgctaa tcacgacgcg ctgtatcgct ggatcaaatc tgtcgatcct 1440 tcccgcccgg tgcagtatga aggcggcgga gccgacacca cggccaccga tattatttgc 1500 ccgatgtacg cgcgcgtgga tgaagaccag cccttcccgg ctgtgccgaa atggtccatc 1560 aaaaaatggc tttcgctacc tggagagacg cgcccgctga tcctttgcga atacgcccac 1620 gcgatgggta acagtcttgg cggtttcgct aaatactggc aggcgtttcg tcagtatccc 1680 cgtttacagg gcggcttcgt ctgggactgg gtggatcagt cgctgattaa atatgatgaa 1740 aacggcaacc cgtggtcggc ttacggcggt gattttggcg atacgccgaa cgatcgccag 1800 ttctgtatga acggtctggt ctttgccgac cgcacgccgc atccagcgct gacggaagca 1860 aaacaccagc agcagttttt ccagttccgt ttatccgggc aaaccatcga agtgaccagc 1920 gaatacctgt tccgtcatag cgataacgag ctcctgcact ggatggtggc gctggatggt 1980 aagccgctgg caagcggtga agtgcctctg gatgtcgctc cacaaggtaa acagttgatt 2040 gaactgcctg aactaccgca gccggagagc gccgggcaac tctggctcac agtacgcgta 2100 gtgcaaccga acgcgaccgc atggtcagaa gccgggcaca tcagcgcctg gcagcagtgg 2160 cgtctggcgg aaaacctcag tgtgacgctc cccgccgcgt cccacgccat cccgcatctg 2220 accaccagcg aaatggattt ttgcatcgag ctgggtaata agcgttggca atttaaccgc 2280 cagtcaggct ttctttcaca gatgtggatt ggcgataaaa aacaactgct gacgccgctg 2340 cgcgatcagt tcacccgtgc accgctggat aacgacattg gcgtaagtga agcgacccgc 2400 attgacccta acgcctgggt cgaacgctgg aaggcggcgg gccattacca ggccgaagca 2460 gcgttgttgc agtgcacggc agatacactt gctgatgcgg tgctgattac gaccgctcac 2520 gcgtggcagc atcaggggaa aaccttattt atcagccgga aaacctaccg gattgatggt 2580 agtggtcaaa tggcgattac cgttgatgtt gaagtggcga gcgatacacc gcatccggcg 2640 cggattggcc tgaactgcca gctggcgcag gtagcagagc gggtaaactg gctcggatta 2700 gggccgcaag aaaactatcc cgaccgcctt actgccgcct gttttgaccg ctgggatctg 2760 ccattgtcag acatgtatac cccgtacgtc ttcccgagcg aaaacggtct gcgctgcggg 2820 acgcgcgaat tgaattatgg cccacaccag tggcgcggcg acttccagtt caacatcagc 2880 cgctacagtc aacagcaact gatggaaacc agccatcgcc atctgctgca cgcggaagaa 2940 ggcacatggc tgaatatcga cggtttccat atggggattg gtggcgacga ctcctggagc 3000 ccgtcagtat cggcggaatt ccagctgagc gccggtcgct accattacca gttggtctgg 3060 tgtcaaaaat aataataa 3078 // Output file format Output files for usage example File: globins.infoalign # USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3 4 68 17 61 54.666668 0.610000 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3 4 68 17 61 54.666668 0.650000 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2 3 60 9 72 58.333332 0.650000 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2 3 63 6 72 56.250000 0.830000 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3 4 30 15 108 80.891716 1.000000 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1 2 32 16 101 78.807945 0.910000 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 19 24 110 87.581696 0.430000 Output files for usage example 2 File: globins.infoalign # Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description HBB_HUMAN 146 150 3 4 68 17 61 54.66666 8 0.610000 HBB_HORSE 146 150 3 4 68 17 61 54.66666 8 0.650000 HBA_HUMAN 141 144 2 3 60 9 72 58.33333 2 0.650000 HBA_HORSE 141 144 2 3 63 6 72 56.25000 0 0.830000 MYG_PHYCA 153 157 3 4 30 15 108 80.89171 6 1.000000 GLB5_PETMA 149 151 1 2 32 16 101 78.80794 5 0.910000 LGB2_LUPLU 153 153 0 0 19 24 110 87.58169 6 0.430000 Output files for usage example 3 File: globins.infoalign HBB_HUMAN 146 HBB_HORSE 146 HBA_HUMAN 141 HBA_HORSE 141 MYG_PHYCA 153 GLB5_PETMA 149 LGB2_LUPLU 153 Output files for usage example 4 File: globins.infoalign HBB_HUMAN 4 61 HBB_HORSE 4 61 HBA_HUMAN 3 72 HBA_HORSE 3 72 MYG_PHYCA 4 108 GLB5_PETMA 2 101 LGB2_LUPLU 0 110 Output files for usage example 5 File: globins.infoalign HBB_HUMAN 3 HBB_HORSE 3 HBA_HUMAN 2 HBA_HORSE 2 MYG_PHYCA 3 GLB5_PETMA 1 LGB2_LUPLU 0 Output files for usage example 6 File: globins.infoalign
USANameSequence LengthAligned Length GapsGap LengthIdentitySimilarityDifference% ChangeWeightDescription
msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3 4 68 17 61 54.666668 0.610000
msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3 4 68 17 61 54.666668 0.650000
msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2 3 60 9 72 58.333332 0.650000
msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2 3 63 6 72 56.250000 0.830000
msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3 4 30 15 108 80.891716 1.000000
msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1 2 32 16 101 78.807945 0.910000
msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 19 24 110 87.581696 0.430000
Output files for usage example 7 File: globins.infoalign # USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description msf::../../data/globins.msf:HBB_HUMAN HBB_HUMAN 146 150 3 4 146 0 0 2.666667 0.610000 msf::../../data/globins.msf:HBB_HORSE HBB_HORSE 146 150 3 4 122 10 14 18.666666 0.650000 msf::../../data/globins.msf:HBA_HUMAN HBA_HUMAN 141 144 2 3 48 19 74 66.666664 0.650000 msf::../../data/globins.msf:HBA_HORSE HBA_HORSE 141 144 2 3 51 18 72 64.583336 0.830000 msf::../../data/globins.msf:MYG_PHYCA MYG_PHYCA 153 157 3 4 30 22 101 80.891716 1.000000 msf::../../data/globins.msf:GLB5_PETMA GLB5_PETMA 149 151 1 2 24 27 98 84.105957 0.910000 msf::../../data/globins.msf:LGB2_LUPLU LGB2_LUPLU 153 153 0 0 21 28 104 86.274513 0.430000 Output files for usage example 8 File: test.out # USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description tembl-id:J01636 J01636 7477 7477 0 0 374 0 7103 94.997993 1.000000 E.coli lactose operon with lacI, lacZ, l acY and lacA genes. tembl-id:X51872 X51872 1832 1832 0 0 374 0 1458 79.585152 1.000000 Escherichia coli lacA gene for thiogalac toside transacetylase tembl-id:V00294 V00294 1113 1113 0 0 302 0 811 72.866127 1.000000 E. coli laci gene (codes for the lac rep ressor). tembl-id:V00295 V00295 1500 1500 0 0 336 0 1164 77.599998 1.000000 E. coli lacY gene (codes for lactose per mease). tembl-id:V00296 V00296 3078 3078 0 0 373 0 2705 87.881744 1.000000 E. coli gene lacZ coding for beta-galact osidase (EC 3.2.1.23). Output files for usage example 9 File: test.out # USA Name SeqLen AlignLen Gaps GapLen Ident Similar Differ % Change Weight Description tembl-id:V00296 V00296 3078 3078 0 0 3078 0 0 0.000000 1.000000 E. coli gene lacZ coding for beta-galact osidase (EC 3.2.1.23). The first non-blank line is the heading. This is followed by one line per sequence containing the following columns of data separated by one of more space or TAB characters: * The USA (Uniform Sequence Address) that EMBOSS can use to read in the sequence. * Name - name of the sequence. * SeqLen - length of the sequence when all gap characters are removed. * AlignLen - length of the sequence including internal gap characters i.e. gaps at the start or the end are not included. * Gaps - number of gaps e.g. 'AAA---AAA' is 1 gap (and 3 gap characters long (see GapLen)). * GapLen - total number of internal gap characters, see the 3 gap characters above. This is the sum total of all of the internal gap characters in this sequence. * Ident - number of characters that are identical to the specified reference sequence (uppercase 'A' is identical to lowercase 'a'). * Similar - number of characters which are non-identical - which score > 0 in the comparison matrix when compared to the reference sequence, but which are not identical. * Different - number of characters which score <= 0 in the comparison matrix when compared to the reference sequence. * %Change - a simple measure of the percentage change as compared to the reference sequence: (AlignLen - Ident) * 100 / AlignLen * Description - the description annotation of the sequence (if any). If qualifiers to inhibit various columns of information are used, then the remaining columns of information are output in the same order as shown above, so if '-noseqlength' is used, the order of output is: usa, name, alignlength, gaps, gapcount, idcount, simcount, diffcount, change, description. When the -html qualifier is specified, then the output will be wrapped in HTML tags, ready for inclusion in a Web page. Note that tags such as and are not output by this program as the table of databases is expected to form only part of the contents of a web page - the rest of the web page must be supplier by the user. The lines of output information are guaranteed not to have trailing white-space at the end. Data files infoalign reads in scoring matrices to determine the consensus sequence and to determine which matches are similar or not. EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA. To see the available EMBOSS data files, run: % embossdata -showall To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run: % embossdata -fetch -file Exxx.dat Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put 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 Notes There are many qualifiers to control exactly what information on the sequence is output and how it is formatted. If you only want a few fields in the output file, the command line may be shortended by preceding the appropriate qualifier with -only. For example, instead of specifying -nohead -nousa -noname -noalign -nogaps -nogapcount -nosimcount -noidcount -nodiffcount -noweight to get only the sequence length output, you can specify -only -seqlength. By default, the output file starts each line with the USA of the sequence being described, so the output file is a list file that can be manually edited and read in by any other EMBOSS program that can read in one or more sequence to be analysed. References None. Warnings None. Diagnostic Error Messages None. Exit status It always exits with status 0. Known bugs None. See also Program name Description abiview Display the trace in an ABI sequencer file coderet Extract CDS, mRNA and translations from feature tables edialign Local multiple alignment of sequences emma Multiple sequence alignment (ClustalW wrapper) entret Retrieve sequence entries from flatfile databases and files extractalign Extract regions from a sequence alignment infoseq Display basic information about sequences plotcon Plot conservation of a sequence alignment prettyplot Draw a sequence alignment with pretty formatting refseqget Get reference sequence seqxref Retrieve all database cross-references for a sequence entry seqxrefget Retrieve all cross-referenced data for a sequence entry showalign Display a multiple sequence alignment in pretty format tranalign Generate an alignment of nucleic coding regions from aligned proteins variationget Get sequence variations whichdb Search all sequence databases for an entry and retrieve it Author(s) Gary Williams formerly at: MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Written (June 2001) - Gary Williams Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None