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ehmmalign |
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Function
Align sequences to an HMM profileDescription
EMBASSY HMMER is a suite of application wrappers to the original hmmer v2.3.2 applications written by Sean Eddy. hmmer v2.3.2 must be installed on the same system as EMBOSS and the location of the hmmer executables must be defined in your path for EMBASSY HMMER to work.Usage:
ehmmalign [options] hmmfile seqfile outfile
The outfile parameter is new to EMBASSY HMMER. The multiple sequence alignment is always written to outfile. The name of outfile is specified by the -o option as normal.
hmmalign reads an HMM profile
Algorithm
Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory.Usage
Here is a sample session with ehmmalign
% ehmmalign ../ehmmcalibrate-ex-keep/globino.hmm globins630.fa globins630.ali Align sequences to an HMM profile hmmalign - align sequences to an HMM profile HMMER 2.3.2 (Oct 2003) Copyright (C) 1992-2003 HHMI/Washington University School of Medicine Freely distributed under the GNU General Public License (GPL) - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - HMM file: ../ehmmcalibrate-ex-keep/globino.hmm Sequence file: ./ehmmalign-1234567890.1234 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Alignment saved in file globins630.ali /shared/software/bin/hmmalign --informat FASTA --outformat A2M -o globins630.ali ../ehmmcalibrate-ex-keep/globino.hmm ./ehmmalign-1234567890.1234 |
Go to the input files for this example
Go to the output files for this example
Command line arguments
Where possible, the same command-line qualifier names and parameter order is used as in the original hmmer. There are however several unavoidable differences and these are clearly documented in the "Notes" section below.More or less all options documented as "expert" in the original hmmer user guide are given in ACD as "advanced" options (-options must be specified on the command-line in order to be prompted for a value for them).
Align sequences to an HMM profile Version: EMBOSS:6.3.0 Standard (Mandatory) qualifiers: [-hmmfile] infile File containing a HMM profile [-seqfile] seqset File containing a (set of) sequence(s) [-o] align [*.ehmmalign] Multiple sequence alignment output file. Additional (Optional) qualifiers: -m boolean [N] Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. -q boolean [N] Quiet; suppress all output except the alignment itself. Useful for piping or redirecting the output. Advanced (Unprompted) qualifiers: -mapali infile Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a 'map' kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file must be exactly the alignment that the HMM was built from. Compare the -withali option. -withali infile Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. Compare the -mapali option. Associated qualifiers: "-seqfile" 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 "-o" 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 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 |
Qualifier | Type | Description | Allowed values | Default |
---|---|---|---|---|
Standard (Mandatory) qualifiers | ||||
[-hmmfile] (Parameter 1) |
infile | File containing a HMM profile | Input file | Required |
[-seqfile] (Parameter 2) |
seqset | File containing a (set of) sequence(s) | Readable set of sequences | Required |
[-o] (Parameter 3) |
align | Multiple sequence alignment output file. | Alignment output file | <*>.ehmmalign |
Additional (Optional) qualifiers | ||||
-m | boolean | Include in the alignment only those symbols aligned to match states. Do not show symbols assigned to insert states. | Boolean value Yes/No | No |
-q | boolean | Quiet; suppress all output except the alignment itself. Useful for piping or redirecting the output. | Boolean value Yes/No | No |
Advanced (Unprompted) qualifiers | ||||
-mapali | infile | Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is defined by a 'map' kept in the HMM, and so is fast and guaranteed to be consistent with the way the HMM was constructed from the alignment. The alignment in the file must be exactly the alignment that the HMM was built from. Compare the -withali option. | Input file | Required |
-withali | infile | Reads an alignment from file and aligns it as a single object to the HMM; e.g. the alignment in file is held fixed. This allows you to align sequences to a model with hmmalign and view them in the context of an existing trusted multiple alignment. The alignment to the alignment is done with a heuristic (nonoptimal) dynamic programming procedure, which may be somewhat slow and is not guaranteed to be completely consistent with the way the HMM was constructed (though it should be quite close). However, any alignment can be used, not just the alignment that the HMM was built from. Compare the -mapali option. | Input file | Required |
Associated qualifiers | ||||
"-seqfile" associated seqset qualifiers | ||||
-sbegin2 -sbegin_seqfile |
integer | Start of each sequence to be used | Any integer value | 0 |
-send2 -send_seqfile |
integer | End of each sequence to be used | Any integer value | 0 |
-sreverse2 -sreverse_seqfile |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
-sask2 -sask_seqfile |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
-snucleotide2 -snucleotide_seqfile |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
-sprotein2 -sprotein_seqfile |
boolean | Sequence is protein | Boolean value Yes/No | N |
-slower2 -slower_seqfile |
boolean | Make lower case | Boolean value Yes/No | N |
-supper2 -supper_seqfile |
boolean | Make upper case | Boolean value Yes/No | N |
-sformat2 -sformat_seqfile |
string | Input sequence format | Any string | |
-sdbname2 -sdbname_seqfile |
string | Database name | Any string | |
-sid2 -sid_seqfile |
string | Entryname | Any string | |
-ufo2 -ufo_seqfile |
string | UFO features | Any string | |
-fformat2 -fformat_seqfile |
string | Features format | Any string | |
-fopenfile2 -fopenfile_seqfile |
string | Features file name | Any string | |
"-o" associated align qualifiers | ||||
-aformat3 -aformat_o |
string | Alignment format | Any string | fasta |
-aextension3 -aextension_o |
string | File name extension | Any string | |
-adirectory3 -adirectory_o |
string | Output directory | Any string | |
-aname3 -aname_o |
string | Base file name | Any string | |
-awidth3 -awidth_o |
integer | Alignment width | Any integer value | 0 |
-aaccshow3 -aaccshow_o |
boolean | Show accession number in the header | Boolean value Yes/No | N |
-adesshow3 -adesshow_o |
boolean | Show description in the header | Boolean value Yes/No | N |
-ausashow3 -ausashow_o |
boolean | Show the full USA in the alignment | Boolean value Yes/No | N |
-aglobal3 -aglobal_o |
boolean | Show the full sequence in alignment | Boolean value Yes/No | N |
General qualifiers | ||||
-auto | boolean | Turn off prompts | Boolean value Yes/No | N |
-stdout | boolean | Write first file to standard output | Boolean value Yes/No | N |
-filter | boolean | Read first file from standard input, write first file to standard output | Boolean value Yes/No | N |
-options | boolean | Prompt for standard and additional values | Boolean value Yes/No | N |
-debug | boolean | Write debug output to program.dbg | Boolean value Yes/No | N |
-verbose | boolean | Report some/full command line options | Boolean value Yes/No | Y |
-help | boolean | Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose | Boolean value Yes/No | N |
-warning | boolean | Report warnings | Boolean value Yes/No | Y |
-error | boolean | Report errors | Boolean value Yes/No | Y |
-fatal | boolean | Report fatal errors | Boolean value Yes/No | Y |
-die | boolean | Report dying program messages | Boolean value Yes/No | Y |
-version | boolean | Report version number and exit | Boolean value Yes/No | N |
Input file format
Alignment and sequence formats
Input and output of alignments and sequences is limited to the formats that the original hmmer supports. These include stockholm, SELEX, MSF, Clustal, Phylip and A2M /aligned FASTA (alignments) and FASTA, GENBANK, EMBL, GCG, PIR (sequences). It would be fairly straightforward to adapt the code to support all EMBOSS-supported formats.Compressed input files
Automatic processing of gzipped files is not supported.ehmmalign reads any normal sequence USAs.
Input files for usage example
File: ../ehmmcalibrate-ex-keep/globino.hmm
HMMER2.0 [2.3.2] NAME globins50 LENG 143 ALPH Amino RF no CS no MAP yes COM /shared/software/bin/hmmbuild -n globins50 --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F globin.hmm ../../data/hmmnew/globins50.msf COM /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex-keep/globin.hmm NSEQ 50 DATE Thu Jul 15 12:00:00 2010 CKSUM 9858 XT -8455 -4 -1000 -1000 -8455 -4 -8455 -4 NULT -4 -8455 NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644 EVD -35.959286 0.267496 HMM A C D E F G H I K L M N P Q R S T V W Y m->m m->i m->d i->m i->i d->m d->d b->m m->e -450 * -1900 1 591 -1587 159 1351 -1874 -201 151 -1600 998 -1591 -693 389 -1272 595 42 -31 27 -693 -1797 -1134 14 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 -450 * 2 -926 -2616 2221 2269 -2845 -1178 -325 -2678 -300 -2596 -1810 220 -1592 939 -974 -671 -939 -2204 -2785 -1925 15 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 3 -638 -1715 -680 497 -2043 -1540 23 -1671 2380 -1641 -840 -222 -1595 437 1040 -564 -523 -1363 2124 -1313 16 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 4 829 -1571 -37 660 -1856 -873 152 -1578 894 -1573 -678 769 -1273 1284 58 224 447 -1175 -1782 -1125 17 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 5 369 -433 -475 286 -974 -1312 -19 -412 664 398 406 1030 -1394 388 -214 -261 85 -166 -1227 -725 18 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 6 -1291 -884 -3696 -3261 -1137 -3425 -2802 2322 -3066 111 19 -3028 -3275 -2855 -3100 -2670 -1269 2738 -2450 -2062 19 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 7 157 -413 -236 316 -1387 -1231 89 -863 1084 -431 -348 910 -1319 635 297 15 704 -483 -1497 -922 20 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 8 770 -1431 -43 459 -1751 -340 78 -1449 440 -1497 -631 866 -1302 825 -51 953 364 -1076 -1750 -1121 21 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 9 420 -186 -2172 -1577 8 -1818 -694 1477 -1281 760 614 -1299 -1867 -1001 -1262 -189 -12 1401 -722 -364 22 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 10 -961 -879 -2277 -1821 1366 -2213 -204 -399 -1500 -130 -39 -1427 -2266 -1186 -1511 -159 -913 -367 4721 1177 23 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 11 -48 -1782 809 844 -2073 1456 8 -1811 315 -1803 -932 180 -1365 921 -218 173 -115 -1399 -2018 -1327 24 [Part of this file has been deleted for brevity] - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 128 -415 -1926 1575 1399 -2219 -1163 17 -1983 527 -1929 -1039 341 -1367 1597 -212 257 -222 -1536 -2109 -1387 144 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 129 -529 -1434 -629 -143 -1926 -626 -171 -1460 2679 -1597 -839 -309 -1599 207 317 -530 -510 -130 -1840 -1369 145 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 130 811 -397 -2389 -1807 1883 -2039 -907 594 -1512 1077 687 -1532 -2065 -1201 -1483 -1125 -465 1067 -843 -472 146 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 131 -241 -102 -2327 -1710 724 -1767 -616 650 -1363 1074 1765 -718 -1809 -1026 -1252 -842 -181 1331 -541 695 147 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 132 723 95 385 823 -1820 -1168 167 -1540 875 -1362 -644 320 -1261 810 246 693 -67 -1141 -1753 -1098 148 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 133 551 -430 -1049 -481 -442 469 -241 465 -313 133 947 -411 -1543 197 -587 -146 202 522 -843 -429 149 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 134 -1086 -777 -3351 -2800 816 -2898 -1861 1501 -2515 1149 586 -2483 -2775 -2108 -2400 -2046 -1030 2380 -1511 -1216 150 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 135 1393 1409 -876 -345 -997 -525 -315 -590 -198 -847 -109 -420 -1441 -97 412 766 -130 139 -1306 -858 151 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6528 -7571 -894 -1115 -701 -1378 * * 136 98 -1299 36 365 -1495 -1211 1241 -404 523 -952 -426 1174 -1303 511 -18 347 882 -853 -1566 -970 152 - 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-22 -6602 -7644 -894 -1115 -701 -1378 * * 141 351 -1646 -165 546 -1976 -498 46 -1667 2193 -1662 -798 35 -1405 476 311 -73 -306 -1287 -1859 -1254 157 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -23 -6561 -7603 -894 -1115 -701 -1378 * * 142 -1995 -1606 -3095 -2870 1739 -3015 -98 -1012 -2520 -730 655 -1990 -2962 -1884 -2326 -2167 -1915 -1128 548 4089 158 - -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249 - -25 -6455 -7497 -894 -1115 -701 -1378 * * 143 -253 -1373 -267 301 -911 -565 1956 -450 1188 -1330 -497 33 -1352 502 1358 -205 -184 -941 -1604 -1026 159 - * * * * * * * * * * * * * * * * * * * * - * * * * * * * * 0 // |
File: globins630.fa
> BAHG_VITSP MLDQQTINIIKATVPVLKEHGVTITTTFYKNLFAKHPEVRPLFDMGRQESLEQPKALAM TVLAAAQNIENLPAILPAVKKIAVKHCQAGVAAAHYPIVGQELLGAIKEVLGDAATDDIL DAWGKAYGVIADVfiqveadLYAQAVE > GLB1_ANABR PSVQGAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ GMANDKLRGHSITLMYALQNFIDQLDNTDDLVCVVEKFAVNHITRKISAAEFGKINGPIK KVLASKNFGDKYANAWAKLVAVVQAAL > GLB1_ARTSX ERVDPITGLSGLEKNAILDTWGKVRGNLQEVGKATFGKLFAAHPEYQQMFRFFQGVQLA FLVQSPKFAAHTQRVVSALDQTLLALNRPSDQFVYMIKELGLDHINRGTDRSFVEYLKES LGDSVDEFTVQSFGEVIVNFLNEGLRQA > GLB1_CALSO VSANDIKNVQDTWGKLYDQWDAVHAsKFYNKLFKDSEDISEAFVKAGTGSGIAMKRQAL VFGAILQEFVANLNDPTALTLKIKGLCATHKTRGITNMELFAFALADLVAYMGTtISFTA AQKASWTAVNDVILHQMSSYFATVA > GLB1_CHITH GPSGDQIAAAKASWNTVKNNQVDILYAVFKANPDIQTAFSQFAGKDLDSIKGTPDFSKH AGRVVGLFSEVMDLLGNDANTPTILAKAKDFGKSHKSRASPAQLDNFRKSLVVYLKGATK WDSAVESSWAPVLDFVFSTLKNEL > GLB1_GLYDI GLSAAQRQVIAATWKDIAGADNGAGVGKDCLIKFLSAHPQMAAVFGFSGASDPGVAALG AKVLAQIGVAVSHLGDEGKMVAQMKAVGVRHKGYGNKHIKAQYFEPLGASLLSAMEHRIG GKMNAAAKDAWAAAYADISGALISGLQS > GLB1_LUMTE ECLVTEGLKVKLQWASAFGHAHQRVAFGLELwkgILREHPEIKAPFSRVRGDNIYSPQF GAHSQRVLSGLDITISMLDTPDmLAAQLAHLKVQHVERNLKPEFFDIFLKHLLHVLGDRL GTHFDFGAWHDCVDQIIDGIKDI > GLB1_MORMR PIVDSGSVSPLSDAEKNKIRAAWDLVYKDYEKTGVDILVKFFTGTPAAQAFFPKFKGLT TADDLKQSSDVRWHAERIINAVNDAVKSMDDTEKMSMKLKELSIKHAQSFYVDRQYFKVL AGIIADTTAPGDAGFEKLMSMICILLSSAY > GLB1_PARCH GGTLAIQSHGDLTLAQKKIVRKTWHQLMRNKTSFVTDLFIRIFAYDPAAQNKFPQMAGM SASQLRSSRQMQAHAIRVSSIMSEYIEELDSDILPELLATLARTHDLNKVGPAHYDLFAK VLMEALQAELGSDFNQKTRDSWAKAFSIVQAVLLVKHG > GLB1_PETMA PIVDSGSVPALTAAEKATIRTAWAPVYAKYQSTGVDILIKFFTSNPAAQAFFPKFQGLT SADQLKKSMDVRWHAERIINAVNDAVVAMDDTEKMSLKLRELSGKHAKSFQVDPQYFKVL AAVIVDTVLPGDAGLEKLMSMICILLRSSY > GLB1_PHESE DCNTLKRFKVKHQWQQVFSGEhHRTEFSLHFWKEFLHDHPDLVSLFKRVQGENIYSPEF QAHGIRVLAGLDSVIGVLDEDDTFTVQLAHLKAQHTERGTKPEYFDLFGTQLFDILGDKL GTHFDQAAWRDCYAVIAAGIKP > GLB1_SCAIN PSVYDAAAQLTADVKKDLRDSWKVIGSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQ GMANDKLRGHSITLMYALQNFIDQLDNPDDLVCVVEKFAVNHITRKISAAEFGKINGPIK KVLASKNFGDKYANAWAKLVAVVQAAL > GLB1_TYLHE TDCGILQRIKVKQQWAQVYSVGESRTDFAIDVFNNFFRTNPDRSLFNRVNGDNVYSPEF [Part of this file has been deleted for brevity] GLSDAEWQLVLNVWGKVEADLAGHGQEVLIRLFHTHPETLEKFDKFKHLKSEDEMKASE DLKKHGNTVLTALGAILKKKGHHEAEIKPLAQSHATKHKIPVKYLEFISEAIIHVLHSKH PGDFGADAQAAMSKALELFRNDIAAQYKELGFQG > MYG_ROUAE GLSDGEWQLVLNVWGKVEADIPGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKASE DLKKHGATVLTALGGILKKKGQHEAQLKPLAQSHATKHKIPVKYLEFISEVIIQVLQSKH PGDFGADAQGAMGKALELFRNDIAAKYKELGFQG > MYG_SAISC GLSDGEWQLVLNIWGKVEADIPSHGQEVLISLFKGHPETLEKFDKFKHLKSEDEMKASE ELKKHGTTVLTALGGILKKKGQHEAELKPLAQSHATKHKIPVKYLELISDAIVHVLQKKH PGDFGADAQGAMKKALELFRNDMAAKYKELGFQG > MYG_SHEEP GLSDGEWQLVLNAWGKVEADVAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASE DLKKHGNTVLTALGGILKKKGHHEAEVKHLAESHANKHKIPVKYLEFISDAIIHVLHAKH PSNFGADAQGAMSKALELFRNDMAAEYKVLGFQG > MYG_SPAEH GLSDGEWQLVLNVWGKVEGDLAGHGQEVLIKLFKNHPETLEKFDKFKHLKSEDEMKGSE DLKKHGNTVLTALGGILKKKGQHAAEIQPLAQSHATKHKIPIKYLEFISEAIIQVLQSKH PGDFGADAQGAMSKALELFRNDIAAKYKELGFQG > MYG_TACAC GLSDGEWQLVLKVWGKVETDITGHGQDVLIRLFKTHPETLEKFDKFKHLKTEDEMKASA DLKKHGGVVLTALGSILKKKGQHEAELKPLAQSHATKHKISIKFLEFISEAIIHVLQSKH SADFGADAQAAMGKALELFRNDMATKYKEFGFQG > MYG_THUAL ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAH GATVLKKLGELLKAKGSHAAILKPLANSHATKHKIPINNFKLISEVLVKVMHEKAGLDAG GQTALRNVMGIIIADLEANYKELGFSG > MYG_TUPGL GLSDGEWQLVLNVWGKVEADVAGHGQEVLIRLFKGHPETLEKFDKFKHLKTEDEMKASE DLKKHGNTVLSALGGILKKKGQHEAEIKPLAQSHATKHKIPVKYLEFISEAIIQVLQSKH PGDFGADAQAAMSKALELFRNDIAAKYKELGFQG > MYG_TURTR GLSDGEWQLVLNVWGKVEADLAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEADMKASE DLKKHGNTVLTALGAILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRH PAEFGADAQGAMNKALELFRKDIAAKYKELGFHG > MYG_VARVA GLSDEEWKKVVDIWGKVEPDLPSHGQEVIIRMFQNHPETQDRFAKFKNLKTLDEMKNSE DLKKHGTTVLTALGRILKQKGHHEAEIAPLAQTHANTHKIPIKYLEFICEVIVGVIAEKH SADFGADSQEAMRKALELFRNDMASRYKELGFQG > MYG_VULCH GLSDGEWQLVLNIWGKVETDLAGHGQEVLIRLFKNHPETLDKFDKFKHLKTEDEMKGSE DLKKHGNTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPVKYLEFISDAIIQVLQSKH SGDFHADTEAAMKKALELFRNDIAAKYKELGFQG > MYG_ZALCA GLSDGEWQLVLNIWGKVEADLVGHGQEVLIRLFKGHPETLEKFDKFKHLKSEDEMKRSE DLKKHGKTVLTALGGILKKKGHHDAELKPLAQSHATKHKIPIKYLEFISEAIIHVLQSKH PGDFGADTHAAMKKALELFRNDIAAKYRELGFQG > MYG_ZIPCA GLSEAEWQLVLHVWAKVEADLSGHGQEILIRLFKGHPETLEKFDKFKHLKSEAEMKASE DLKKHGHTVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRH PSDFGADAQAAMTKALELFRKDIAAKYKELGFHG |
Output file format
ehmmalign outputs a graph to the specified graphics device. outputs a report format file. The default format is ...Output files for usage example
File: globins630.ali
>BAHG_VITSP .................mldqQTINIIKATV.PV...L.....K...E...H...GV.T. ....I...TTTFYKN..LFAKHPEVRPLFDMGRQESL-------..EQPKALAMTVLAAA QN-IENLPA......ILPAVKKIAVKH..CQAG-..VAAAHYPIV.GQELLGAIKEV.L. G.D.AATDDILDAWGKAYGVIADVFIQVEAdlyaqave >GLB1_ANABR .........psvqgaaaqltaDVKKDLRDSW.KV...I.....G...S...D...KK.G. ....N...GVALMTT..LFADNQETIGYFKRLGNVSQ---GMAN..DKLRGHSITLMYAL QNFIDQLDNt...ddLVCVVEKFAVNH..ITR-K..ISAAEFGKI.NGPIKKVLAS-.-. -.K.NFGDKYANAWAKLVAVVQAAL-----........ >GLB1_ARTSX ..........ervdpitglsgLEKNAILDTW.GK...V.....R...G...N...LQ.E. ....V...GKATFGK..LFAAHPEYQQMFRFFQGVQL-AFLVQS..PKFAAHTQRVVSAL DQTLLALNRps..dqFVYMIKELGLDH..INRGT..-DRSFVEYL.KESL-----GD.S. V.D.EFT------VQSFGEVIVNFLNEGLRqa...... >GLB1_CALSO ..................vsaNDIKNVQDTW.GK...L.....Y...D...Q...WD.A. ....V..hASKFYNK..LFKDSEDISEAFVKAGT---GSGIAMK..RQALVFGA-ILQEF VANLNDPTA......LTLKIKGLCATH..KTRGI..TNMELFAFA.LADLVAYMGTT.I. S.-.-FTAAQKASWTAVNDVILHQMSSYFAtva..... >GLB1_CHITH .................gpsgDQIAAAKASW.NT...V.....-...-...-...-K.N. ....N...QVDILYA..VFKANPDIQTAFSQFAG-KDLDSIKGT..PDFSKHAGRVVGLF SEVMDLLGNdantptILAKAKDFGKSH..--KSR..ASPAQLDNF.RKSLVVYLKGA.-. -.T.KWDSAVESSWAPVLDFVFSTLKNEL-........ >GLB1_GLYDI .................glsaAQRQVIAATW.KD...I.....A...Ga.dN...GA.G. ....V...GKDCLIK..FLSAHPQMAAVFGFSGA--------SD..PGVAALGAKVLAQI GVAVSHLGDe...gkMVAQMKAVGVRHkgYGNKH..IKAQYFEPL.GASLLSAMEHR.I. G.G.KMNAAAKDAWAAAYADISGALISGLQs....... >GLB1_LUMTE .............eclvteglKVKLQWASAF.GH...A.....-...H...Q...RV.A. ....F...GLELWKG..ILREHPEIKAPFSRVRG-DN----IYS..PQFGAHSQRVLSGL DITISMLDTp...dmLAAQLAHLKVQH..VER-N..LKPEFFDIF.LKHLLHVLGDR.L. G.T.HFDF---GAWHDCVDQIIDGIKD--I........ >GLB1_MORMR ........pivdsgsvsplsdAEKNKIRAAW.DL...V.....Y...K...D...YE.K. ....T...GVDILVK..FFTGTPAAQAFFPKFKGLTTADDLKQS..SDVRWHAERIINAV NDAVKSMDDt...ekMSMKLKELSIKH..AQSFY..VDRQYFKVL.AGII-------.-. -.A.DTTAPGDAGFEKLMSMICILLSSAY-........ >GLB1_PARCH .......ggtlaiqshgdltlAQKKIVRKTW.HQ...L.....M...R...N...KT.S. ....F...VTDLFIR..IFAYDPAAQNKFPQMAGMSA-SQLRSS..RQMQAHAIRVSSIM SEYIEELDSd....iLPELLATLARTH..-DLNK..VGPAHYDLF.AKVLMEALQAE.L. G.S.DFNQKTRDSWAKAFSIVQAVLLVKHG........ >GLB1_PETMA ........pivdsgsvpaltaAEKATIRTAW.AP...V.....Y...A...K...YQ.S. ....T...GVDILIK..FFTSNPAAQAFFPKFQGLTSADQLKKS..MDVRWHAERIINAV NDAVVAMDDt...ekMSLKLRELSGKH..AKSFQ..VDPQYFKVL.AAVI-------.-. -.V.DTVLPGDAGLEKLMSMICILLRSSY-........ [Part of this file has been deleted for brevity] P.G.DFGADAQGAMKKALELFRNDMAAKYKelgfqg.. >MYG_SHEEP .................glsdGEWQLVLNAW.GK...V.....E...A...D...VA.G. ....H...GQEVLIR..LFTGHPETLEKFDKFKHLKTEAEMKAS..EDLKKHGNTVLTAL GGILKKKGH......HEAEVKHLAESH..ANKHK..IPVKYLEFI.SDAIIHVLHAK.H. P.S.NFGADAQGAMSKALELFRNDMAAEYKvlgfqg.. >MYG_SPAEH .................glsdGEWQLVLNVW.GK...V.....E...G...D...LA.G. ....H...GQEVLIK..LFKNHPETLEKFDKFKHLKSEDEMKGS..EDLKKHGNTVLTAL GGILKKKGQ......HAAEIQPLAQSH..ATKHK..IPIKYLEFI.SEAIIQVLQSK.H. P.G.DFGADAQGAMSKALELFRNDIAAKYKelgfqg.. >MYG_TACAC .................glsdGEWQLVLKVW.GK...V.....E...T...D...IT.G. ....H...GQDVLIR..LFKTHPETLEKFDKFKHLKTEDEMKAS..ADLKKHGGVVLTAL GSILKKKGQ......HEAELKPLAQSH..ATKHK..ISIKFLEFI.SEAIIHVLQSK.H. S.A.DFGADAQAAMGKALELFRNDMATKYKefgfqg.. >MYG_THUAL .....................ADFDAVLKCW.GP...V.....E...A...D...YT.T. ....M...GGLVLTR..LFKEHPETQKLFPKFAGIAQ-ADIAGN..AAISAHGATVLKKL GELLKAKGS......HAAILKPLANSH..ATKHK..IPINNFKLI.SEVLVKVMHEK.A. G.-.-LDAGGQTALRNVMGIIIADLEANYKelgfsg.. >MYG_TUPGL .................glsdGEWQLVLNVW.GK...V.....E...A...D...VA.G. ....H...GQEVLIR..LFKGHPETLEKFDKFKHLKTEDEMKAS..EDLKKHGNTVLSAL GGILKKKGQ......HEAEIKPLAQSH..ATKHK..IPVKYLEFI.SEAIIQVLQSK.H. P.G.DFGADAQAAMSKALELFRNDIAAKYKelgfqg.. >MYG_TURTR .................glsdGEWQLVLNVW.GK...V.....E...A...D...LA.G. ....H...GQDVLIR..LFKGHPETLEKFDKFKHLKTEADMKAS..EDLKKHGNTVLTAL GAILKKKGH......HDAELKPLAQSH..ATKHK..IPIKYLEFI.SEAIIHVLHSR.H. P.A.EFGADAQGAMNKALELFRKDIAAKYKelgfhg.. >MYG_VARVA .................glsdEEWKKVVDIW.GK...V.....E...P...D...LP.S. ....H...GQEVIIR..MFQNHPETQDRFAKFKNLKTLDEMKNS..EDLKKHGTTVLTAL GRILKQKGH......HEAEIAPLAQTH..ANTHK..IPIKYLEFI.CEVIVGVIAEK.H. S.A.DFGADSQEAMRKALELFRNDMASRYKelgfqg.. >MYG_VULCH .................glsdGEWQLVLNIW.GK...V.....E...T...D...LA.G. ....H...GQEVLIR..LFKNHPETLDKFDKFKHLKTEDEMKGS..EDLKKHGNTVLTAL GGILKKKGH......HEAELKPLAQSH..ATKHK..IPVKYLEFI.SDAIIQVLQSK.H. S.G.DFHADTEAAMKKALELFRNDIAAKYKelgfqg.. >MYG_ZALCA .................glsdGEWQLVLNIW.GK...V.....E...A...D...LV.G. ....H...GQEVLIR..LFKGHPETLEKFDKFKHLKSEDEMKRS..EDLKKHGKTVLTAL GGILKKKGH......HDAELKPLAQSH..ATKHK..IPIKYLEFI.SEAIIHVLQSK.H. P.G.DFGADTHAAMKKALELFRNDIAAKYRelgfqg.. >MYG_ZIPCA .................glseAEWQLVLHVW.AK...V.....E...A...D...LS.G. ....H...GQEILIR..LFKGHPETLEKFDKFKHLKSEAEMKAS..EDLKKHGHTVLTAL GGILKKKGH......HEAELKPLAQSH..ATKHK..IPIKYLEFI.SDAIIHVLHSR.H. P.S.DFGADAQAAMTKALELFRKDIAAKYKelgfhg.. |
Data files
None.Notes
1. Command-line arguments
The following original HMMER options are not supported:-h : Use -help to get help information instead. -informat : All common sequence file formats are supported automatically. -oneline : Alignment format output is specified via the ACD file and / or the -aformat command line qualifier. -outformat : Alignment format output is specified via the ACD file and / or the -aformat command line qualifier.
2. Installing EMBASSY HMMER
The EMBASSY HMMER package contains "wrapper" applications providing an EMBOSS-style interface to the applications in the original HMMER package version 2.3.2 developed by Sean Eddy. Please read the file INSTALL in the EMBASSY HMMER package distribution for installation instructions.3. Installing original HMMER
To use EMBASSY HMMER, you will first need to download and install the original HMMER package. Please read the file 00README in the the original HMMER package distribution for installation instructions:WWW home: http://hmmer.wustl.edu/ Distribution: ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
4. Setting up HMMER
For the EMBASSY HMMER package to work, the directory containing the original HMMER executables *must* be in your path. For example if you executables were installed to "/usr/local/hmmer/bin", then type:set path=(/usr/local/hmmer/bin/ $path) rehash
5. Getting help
Please read the Userguide.pdf distributed with the original HMMER and included in the EMBASSY HMMER distribution under the DOCS directory. The first 3 chapters (Introduction, Installation and Tutorial) are particularly useful.Please read the 'Notes' section below for a description of the differences between the original and EMBASSY HMMER, particularly which application command line options are supported.
References
None.Warnings
Types of input data
hmmer v3.2.1 and therefore EMBASSY HMMER is only recommended for use with protein sequences. If you provide a non-protein sequence you will be reprompted for a protein sequence. To accept nucleic acid sequences you must replace instances of < type: "protein" > in the application ACD files withEnvironment variables
The original hmmer uses BLAST environment variables (below), if defined, to locate files. The EMBASSY HMMER does not.BLASTDB location of sequence databases to be searched BLASMAT location of substitution matrices HMMERDB location of HMMs
Sequence input
ehmmalign makes a temporary local copy of its input sequence data. You must ensure there is sufficient disk space for this in the directory that ehmmalign is run.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None.See also
Program name | Description |
---|---|
ehmmbuild | Build a profile HMM from an alignment |
ehmmcalibrate | Calibrate HMM search statistics |
ehmmconvert | Convert between profile HMM file formats |
ehmmemit | Generate sequences from a profile HMM |
ehmmfetch | Retrieve an HMM from an HMM database |
ehmmindex | Create a binary SSI index for an HMM database |
ehmmpfam | Search one or more sequences against an HMM database |
ehmmsearch | Search a sequence database with a profile HMM |
oalistat | Statistics for multiple alignment files |
ohmmalign | Align sequences with an HMM |
ohmmbuild | Build HMM |
ohmmcalibrate | Calibrate a hidden Markov model |
ohmmconvert | Convert between HMM formats |
ohmmemit | Extract HMM sequences |
ohmmfetch | Extract HMM from a database |
ohmmindex | Index an HMM database |
ohmmpfam | Align single sequence with an HMM |
ohmmsearch | Search sequence database with an HMM |
Author(s)
This program is an EMBOSS conversion of a program written by Sean Eddy as part of his HMMER package.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Jon Ison
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
This program is an EMBASSY wrapper to a program written by Sean Eddy as part of his hmmer package.
Please report any bugs to the EMBOSS bug team in the first instance, not to Sean Eddy.