supermatcher 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 Calculate approximate local pair-wise alignments of larger sequences Description supermatcher calculates an approximate alignment between all the sequences in a first set of sequences and all those from a second stream, typically a database. The alignments are written to a standard alignment file. A combination of a word-match and Smith-Waterman local alignment (dynamic programming) algorithms are used. The alignments will be less accurate than an optimal alignment generated by full dynamic programming, but the program will run faster and use less memory, which means it is suitable for use with larger sequences. Usage Here is a sample session with supermatcher % supermatcher @eclac.list tembl:j01636 -word 50 Calculate approximate local pair-wise alignments of larger sequences Gap opening penalty [10.0]: Gap extension penalty [0.5]: 3.0 Output alignment [j01636.supermatcher]: Go to the input files for this example Go to the output files for this example Command line arguments Calculate approximate local pair-wise alignments of larger sequences Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-asequence] seqall Sequence(s) filename and optional format, or reference (input USA) [-bsequence] seqset Sequence set filename and optional format, or reference (input USA) -gapopen float [10.0 for any sequence type] Gap opening penalty (Number from 0.000 to 100.000) -gapextend float [0.5 for any sequence type] Gap extension penalty (Number from 0.000 to 10.000) [-outfile] align [*.supermatcher] Output alignment file name (default -aformat simple) Additional (Optional) qualifiers: -datafile matrixf [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. -minscore float [0] Minimum alignment score to report an alignment. (Number 0.000 or more) -width integer [16] Alignment width (Integer 1 or more) -wordlen integer [6] Word length for initial matching (Integer 3 or more) -errorfile outfile [supermatcher.error] Error file to be written to for failed alignments Advanced (Unprompted) qualifiers: (none) Associated qualifiers: "-asequence" 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 -sformat1 string Input sequence format -sdbname1 string Database name -sid1 string Entryname -ufo1 string UFO features -fformat1 string Features format -fopenfile1 string Features file name "-bsequence" associated qualifiers -sbegin2 integer Start of each sequence to be used -send2 integer End of each sequence to be used -sreverse2 boolean Reverse (if DNA) -sask2 boolean Ask for begin/end/reverse -snucleotide2 boolean Sequence is nucleotide -sprotein2 boolean Sequence is protein -slower2 boolean Make lower case -supper2 boolean Make upper case -sformat2 string Input sequence format -sdbname2 string Database name -sid2 string Entryname -ufo2 string UFO features -fformat2 string Features format -fopenfile2 string Features file name "-outfile" associated qualifiers -aformat3 string Alignment format -aextension3 string File name extension -adirectory3 string Output directory -aname3 string Base file name -awidth3 integer Alignment width -aaccshow3 boolean Show accession number in the header -adesshow3 boolean Show description in the header -ausashow3 boolean Show the full USA in the alignment -aglobal3 boolean Show the full sequence in alignment "-errorfile" associated qualifiers -odirectory 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 supermatcher reads two sets of nucleotide or protein sequences. The input is a standard EMBOSS sequence query (also known as a 'USA'). Major sequence database sources defined as standard in EMBOSS installations include srs:embl, srs:uniprot and ensembl Data can also be read from sequence output in any supported format written by an EMBOSS or third-party application. The input format can be specified by using the command-line qualifier -sformat xxx, where 'xxx' is replaced by 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 further information on sequence formats. Input files for usage example 'tembl:j01636' is a sequence entry in the example nucleic acid database 'tembl' File: eclac.list #Formerly ECLAC tembl:J01636 #Formerly ECLACA tembl:X51872 #Formerly ECLACI tembl:V00294 #Formerly ECLACY tembl:V00295 #Formerly ECLACZ tembl:V00296 Database entry: tembl:j01636 ID J01636; SV 1; linear; genomic DNA; STD; PRO; 7477 BP. XX AC J01636; J01637; K01483; K01793; XX DT 30-NOV-1990 (Rel. 26, Created) DT 09-SEP-2004 (Rel. 81, Last updated, Version 8) XX DE E.coli lactose operon with lacI, lacZ, lacY and lacA genes. XX KW acetyltransferase; beta-D-galactosidase; galactosidase; lac operon; KW lac repressor protein; lacA gene; lacI gene; lactose permease; lacY gene; KW lacZ gene; mutagenesis; palindrome; promoter region; KW thiogalactoside acetyltransferase. XX OS Escherichia coli OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; OC Enterobacteriaceae; Escherichia. XX RN [1] RP 1243-1266 RX DOI; 10.1073/pnas.70.12.3581. RX PUBMED; 4587255. RA Gilbert W., Maxam A.; RT "The nucleotide sequence of the lac operator"; RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3581-3584(1973). XX RN [2] RP 1246-1308 RX DOI; 10.1073/pnas.70.12.3585. RX PUBMED; 4587256. RA Maizels N.M.; RT "The nucleotide sequence of the lactose messenger ribonucleic acid RT transcribed from the UV5 promoter mutant of Escherichia coli"; RL Proc. Natl. Acad. Sci. U.S.A. 70(12):3585-3589(1973). XX RN [3] RX PUBMED; 4598642. RA Gilbert W., Maizels N., Maxam A.; RT "Sequences of controlling regions of the lactose operon"; RL Cold Spring Harb. Symp. Quant. Biol. 38:845-855(1974). XX RN [4] RA Gilbert W., Gralla J., Majors A.J., Maxam A.; RT "Lactose operator sequences and the action of lac repressor"; RL (in) Sund H., Blauer G. (Eds.); RL PROTEIN-LIGAND INTERACTIONS:193-207; RL Walter de Gruyter, New York (1975) XX RN [5] RP 1146-1282 [Part of this file has been deleted for brevity] cgatttggct acatgacatc aaccatatca gcaaaagtga tacgggtatt atttttgccg 4560 ctatttctct gttctcgcta ttattccaac cgctgtttgg tctgctttct gacaaactcg 4620 ggctgcgcaa atacctgctg tggattatta ccggcatgtt agtgatgttt gcgccgttct 4680 ttatttttat cttcgggcca ctgttacaat acaacatttt agtaggatcg attgttggtg 4740 gtatttatct aggcttttgt tttaacgccg gtgcgccagc agtagaggca tttattgaga 4800 aagtcagccg tcgcagtaat ttcgaatttg gtcgcgcgcg gatgtttggc tgtgttggct 4860 gggcgctgtg tgcctcgatt gtcggcatca tgttcaccat caataatcag tttgttttct 4920 ggctgggctc tggctgtgca ctcatcctcg ccgttttact ctttttcgcc aaaacggatg 4980 cgccctcttc tgccacggtt gccaatgcgg taggtgccaa ccattcggca tttagcctta 5040 agctggcact ggaactgttc agacagccaa aactgtggtt tttgtcactg tatgttattg 5100 gcgtttcctg cacctacgat gtttttgacc aacagtttgc taatttcttt acttcgttct 5160 ttgctaccgg tgaacagggt acgcgggtat ttggctacgt aacgacaatg ggcgaattac 5220 ttaacgcctc gattatgttc tttgcgccac tgatcattaa tcgcatcggt gggaaaaacg 5280 ccctgctgct ggctggcact attatgtctg tacgtattat tggctcatcg ttcgccacct 5340 cagcgctgga agtggttatt ctgaaaacgc tgcatatgtt tgaagtaccg ttcctgctgg 5400 tgggctgctt taaatatatt accagccagt ttgaagtgcg tttttcagcg acgatttatc 5460 tggtctgttt ctgcttcttt aagcaactgg cgatgatttt tatgtctgta ctggcgggca 5520 atatgtatga aagcatcggt ttccagggcg cttatctggt gctgggtctg gtggcgctgg 5580 gcttcacctt aatttccgtg ttcacgctta gcggccccgg cccgctttcc ctgctgcgtc 5640 gtcaggtgaa tgaagtcgct taagcaatca atgtcggatg cggcgcgacg cttatccgac 5700 caacatatca taacggagtg atcgcattga acatgccaat gaccgaaaga ataagagcag 5760 gcaagctatt taccgatatg tgcgaaggct taccggaaaa aagacttcgt gggaaaacgt 5820 taatgtatga gtttaatcac tcgcatccat cagaagttga aaaaagagaa agcctgatta 5880 aagaaatgtt tgccacggta ggggaaaacg cctgggtaga accgcctgtc tatttctctt 5940 acggttccaa catccatata ggccgcaatt tttatgcaaa tttcaattta accattgtcg 6000 atgactacac ggtaacaatc ggtgataacg tactgattgc acccaacgtt actctttccg 6060 ttacgggaca ccctgtacac catgaattga gaaaaaacgg cgagatgtac tcttttccga 6120 taacgattgg caataacgtc tggatcggaa gtcatgtggt tattaatcca ggcgtcacca 6180 tcggggataa ttctgttatt ggcgcgggta gtatcgtcac aaaagacatt ccaccaaacg 6240 tcgtggcggc tggcgttcct tgtcgggtta ttcgcgaaat aaacgaccgg gataagcact 6300 attatttcaa agattataaa gttgaatcgt cagtttaaat tataaaaatt gcctgatacg 6360 ctgcgcttat caggcctaca agttcagcga tctacattag ccgcatccgg catgaacaaa 6420 gcgcaggaac aagcgtcgca tcatgcctct ttgacccaca gctgcggaaa acgtactggt 6480 gcaaaacgca gggttatgat catcagccca acgacgcaca gcgcatgaaa tgcccagtcc 6540 atcaggtaat tgccgctgat actacgcagc acgccagaaa accacggggc aagcccggcg 6600 atgataaaac cgattccctg cataaacgcc accagcttgc cagcaatagc cggttgcaca 6660 gagtgatcga gcgccagcag caaacagagc ggaaacgcgc cgcccagacc taacccacac 6720 accatcgccc acaataccgg caattgcatc ggcagccaga taaagccgca gaaccccacc 6780 agttgtaaca ccagcgccag cattaacagt ttgcgccgat cctgatggcg agccatagca 6840 ggcatcagca aagctcctgc ggcttgccca agcgtcatca atgccagtaa ggaaccgctg 6900 tactgcgcgc tggcaccaat ctcaatatag aaagcgggta accaggcaat caggctggcg 6960 taaccgccgt taatcagacc gaagtaaaca cccagcgtcc acgcgcgggg agtgaatacc 7020 acgcgaaccg gagtggttgt tgtcttgtgg gaagaggcga cctcgcgggc gctttgccac 7080 caccaggcaa agagcgcaac aacggcaggc agcgccacca ggcgagtgtt tgataccagg 7140 tttcgctatg ttgaactaac cagggcgtta tggcggcacc aagcccaccg ccgcccatca 7200 gagccgcgga ccacagcccc atcaccagtg gcgtgcgctg ctgaaaccgc cgtttaatca 7260 ccgaagcatc accgcctgaa tgatgccgat ccccacccca ccaagcagtg cgctgctaag 7320 cagcagcgca ctttgcgggt aaagctcacg catcaatgca ccgacggcaa tcagcaacag 7380 actgatggcg acactgcgac gttcgctgac atgctgatga agccagcttc cggccagcgc 7440 cagcccgccc atggtaacca ccggcagagc ggtcgac 7477 // Output file format The output is a standard EMBOSS alignment file. The results can be output in one of several styles by using the command-line qualifier -aformat xxx, where 'xxx' is replaced by the name of the required format. Some of the alignment formats can cope with an unlimited number of sequences, while others are only for pairs of sequences. The available multiple alignment format names are: multiple, simple, fasta, msf, clustal, mega, meganon, nexus,, nexusnon, phylip, phylipnon, selex, treecon, tcoffee, debug, srs. The available pairwise alignment format names are: pair, markx0, markx1, markx2, markx3, markx10, match, sam, bam, score, srspair See: http://emboss.sf.net/docs/themes/AlignFormats.html for further information on alignment formats. By default the output is in 'simple' format. Output files for usage example File: supermatcher.error File: j01636.supermatcher ######################################## # Program: supermatcher # Rundate: Fri 15 Jul 2011 12:00:00 # Commandline: supermatcher # [-asequence] @../../data/eclac.list # [-bsequence] tembl:j01636 # -wordlen 50 # -gapextend 3.0 # Align_format: simple # Report_file: j01636.supermatcher ######################################## #======================================= # # Aligned_sequences: 2 # 1: J01636 # 2: J01636 # Matrix: EDNAFULL # Gap_penalty: 10.0 # Extend_penalty: 3.0 # # Length: 7477 # Identity: 7477/7477 (100.0%) # Similarity: 7477/7477 (100.0%) # Gaps: 0/7477 ( 0.0%) # Score: 37385.0 # # #======================================= J01636 1 gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgccc 50 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 1 gacaccatcgaatggcgcaaaacctttcgcggtatggcatgatagcgccc 50 J01636 51 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg 100 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 51 ggaagagagtcaattcagggtggtgaatgtgaaaccagtaacgttatacg 100 J01636 101 atgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtg 150 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 101 atgtcgcagagtatgccggtgtctcttatcagaccgtttcccgcgtggtg 150 J01636 151 aaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggc 200 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 151 aaccaggccagccacgtttctgcgaaaacgcgggaaaaagtggaagcggc 200 J01636 201 gatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgg 250 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 201 gatggcggagctgaattacattcccaaccgcgtggcacaacaactggcgg 250 [Part of this file has been deleted for brevity] V00296 2501 tgctgattacgaccgctcacgcgtggcagcatcaggggaaaaccttattt 2550 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 3787 tgctgattacgaccgctcacgcgtggcagcatcaggggaaaaccttattt 3836 V00296 2551 atcagccggaaaacctaccggattgatggtagtggtcaaatggcgattac 2600 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 3837 atcagccggaaaacctaccggattgatggtagtggtcaaatggcgattac 3886 V00296 2601 cgttgatgttgaagtggcgagcgatacaccgcatccggcgcggattggcc 2650 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 3887 cgttgatgttgaagtggcgagcgatacaccgcatccggcgcggattggcc 3936 V00296 2651 tgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta 2700 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 3937 tgaactgccagctggcgcaggtagcagagcgggtaaactggctcggatta 3986 V00296 2701 gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccg 2750 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 3987 gggccgcaagaaaactatcccgaccgccttactgccgcctgttttgaccg 4036 V00296 2751 ctgggatctgccattgtcagacatgtataccccgtacgtcttcccgagcg 2800 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4037 ctgggatctgccattgtcagacatgtataccccgtacgtcttcccgagcg 4086 V00296 2801 aaaacggtctgcgctgcgggacgcgcgaattgaattatggcccacaccag 2850 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4087 aaaacggtctgcgctgcgggacgcgcgaattgaattatggcccacaccag 4136 V00296 2851 tggcgcggcgacttccagttcaacatcagccgctacagtcaacagcaact 2900 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4137 tggcgcggcgacttccagttcaacatcagccgctacagtcaacagcaact 4186 V00296 2901 gatggaaaccagccatcgccatctgctgcacgcggaagaaggcacatggc 2950 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4187 gatggaaaccagccatcgccatctgctgcacgcggaagaaggcacatggc 4236 V00296 2951 tgaatatcgacggtttccatatggggattggtggcgacgactcctggagc 3000 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4237 tgaatatcgacggtttccatatggggattggtggcgacgactcctggagc 4286 V00296 3001 ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattacca 3050 |||||||||||||||||||||||||||||||||||||||||||||||||| J01636 4287 ccgtcagtatcggcggaattccagctgagcgccggtcgctaccattacca 4336 V00296 3051 gttggtctggtgtcaaaaataataataa 3078 |||||||||||||||||||||||||||| J01636 4337 gttggtctggtgtcaaaaataataataa 4364 #--------------------------------------- #--------------------------------------- The file 'supermatcher.error' will contain any errors that occured during the program. This may be that wordmatch could not find any matches hence no suitable start point is found for the smith-waterman calculation. Data files For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAMAT is used. Others can be specified. 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 supermatcher generates approximate local alignments for large sequences. The alignments are approximate because as a first step, all the sequence word matches between two sequences are found. By identifying the highest scoring, non-overlapping matches a set of approximate local alignments are calculated for two sequences. These give the centre points for more acurate Smith-Waterman type alignments in a region of width specified by the user. The use of Smith-Waterman in narrow regions means the alignment overall will be rough, but due to the memory saving much larger sequences can be aligned. For the Swmith-Waterman alignment, the gap open and extension penalties and substition matrix may be specified, the later by default is EBLOSUM62 for protein sequences and EDNAMAT for nucleotide sequence. For the word-match alignment, the word length may be specified. The time required for alignment depends very much on word size. A small word size (e.g. 4) may take a very long time even for short sequences. Much larger word sizes (e.g. 30) will give a very quick result. The default of 16 should give reasonably fast alignments. References None. Warnings supermatcher performs a Smith & Waterman alignment (albeit in a narrow best-matching regions identified by simple word-match) and therefore can use huge amounts of memory if the sequences are large. The longer the sequences and the wider the specified alignment width, the more memory will be used. If the program terminates due to lack of memory you can try running the UNIX command limit to see if your stack or memory usage have been limited and if so, run unlimit, (e.g.: % unlimit stacksize). supermatcher has two sequence inputs. The first (asequence) is a database or large file which is read one sequence at a time. The second (bsequence) is a "sequence set" which is loaded into memory. If one of the inputs has more number of sequences than the other one, specifying the file with many number of sequences first would be useful to decrease the amount of memory used while supermatcher running. Because the alignment is made within a narrow area each side of the 'best' diagonal identified by word-matching, if there are sufficient indels between the two sequences, then the path of the Smith & Waterman alignment can wander outside of this area. Making the width larger can avoid this problem, but you then use more memory. Diagnostic Error Messages None. Exit status It always exits with a status of 0. Known bugs None. See also Program name Description matcher Waterman-Eggert local alignment of two sequences seqmatchall All-against-all word comparison of a sequence set water Smith-Waterman local alignment of sequences wordfinder Match large sequences against one or more other sequences wordmatch Finds regions of identity (exact matches) of two sequences Author(s) Ian Longden formerly at: Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. Please report all bugs to the EMBOSS bug team (emboss-bug (c) emboss.open-bio.org) not to the original author. History Target users This program is intended to be used by everyone and everything, from naive users to embedded scripts. Comments None