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ohmmalign |
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% ohmmalign ../ohmmbuild-keep/globin.hmm globins630.fa globins630.ali Align sequences with an HMM Alignment saved in file globins630.ali |
Go to the input files for this example
Go to the output files for this example
Align sequences with an HMM
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-hmmfile] infile HMMER hidden markov model file
[-sequences] seqset (Aligned) protein sequence set filename and
optional format, or reference (input USA)
[-outfile] outfile [*.ohmmalign] HMMER hmmalign program output
file
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers:
-mapalifile infile HMMER alignment file (optional)
-withalifile infile HMMER heuristic alignment file (optional)
-matchonly boolean [N] Only show match state alignment symbols
Associated qualifiers:
"-sequences" 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
-scircular2 boolean Sequence is circular
-squick2 boolean Read id and sequence only
-sformat2 string Input sequence format
-iquery2 string Input query fields or ID list
-ioffset2 integer Input start position offset
-sdbname2 string Database name
-sid2 string Entryname
-ufo2 string UFO features
-fformat2 string Features format
-fopenfile2 string Features file name
"-outfile" associated qualifiers
-odirectory3 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
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| Qualifier | Type | Description | Allowed values | Default |
|---|---|---|---|---|
| Standard (Mandatory) qualifiers | ||||
| [-hmmfile] (Parameter 1) |
infile | HMMER hidden markov model file | Input file | Required |
| [-sequences] (Parameter 2) |
seqset | (Aligned) protein sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required |
| [-outfile] (Parameter 3) |
outfile | HMMER hmmalign program output file | Output file | <*>.ohmmalign |
| Additional (Optional) qualifiers | ||||
| (none) | ||||
| Advanced (Unprompted) qualifiers | ||||
| -mapalifile | infile | HMMER alignment file (optional) | Input file | Required |
| -withalifile | infile | HMMER heuristic alignment file (optional) | Input file | Required |
| -matchonly | boolean | Only show match state alignment symbols | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-sequences" associated seqset qualifiers | ||||
| -sbegin2 -sbegin_sequences |
integer | Start of each sequence to be used | Any integer value | 0 |
| -send2 -send_sequences |
integer | End of each sequence to be used | Any integer value | 0 |
| -sreverse2 -sreverse_sequences |
boolean | Reverse (if DNA) | Boolean value Yes/No | N |
| -sask2 -sask_sequences |
boolean | Ask for begin/end/reverse | Boolean value Yes/No | N |
| -snucleotide2 -snucleotide_sequences |
boolean | Sequence is nucleotide | Boolean value Yes/No | N |
| -sprotein2 -sprotein_sequences |
boolean | Sequence is protein | Boolean value Yes/No | N |
| -slower2 -slower_sequences |
boolean | Make lower case | Boolean value Yes/No | N |
| -supper2 -supper_sequences |
boolean | Make upper case | Boolean value Yes/No | N |
| -scircular2 -scircular_sequences |
boolean | Sequence is circular | Boolean value Yes/No | N |
| -squick2 -squick_sequences |
boolean | Read id and sequence only | Boolean value Yes/No | N |
| -sformat2 -sformat_sequences |
string | Input sequence format | Any string | |
| -iquery2 -iquery_sequences |
string | Input query fields or ID list | Any string | |
| -ioffset2 -ioffset_sequences |
integer | Input start position offset | Any integer value | 0 |
| -sdbname2 -sdbname_sequences |
string | Database name | Any string | |
| -sid2 -sid_sequences |
string | Entryname | Any string | |
| -ufo2 -ufo_sequences |
string | UFO features | Any string | |
| -fformat2 -fformat_sequences |
string | Features format | Any string | |
| -fopenfile2 -fopenfile_sequences |
string | Features file name | Any string | |
| "-outfile" associated outfile qualifiers | ||||
| -odirectory3 -odirectory_outfile |
string | Output directory | Any string | |
| 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 |
HMMER2.0
NAME GLB2_MORMR
ACC
DESC
LENG 147
ALPH Amino
RF yes
CS yes
MAP yes
COM ohmmbuild ../../data/hmm/globins50.msf globin.hmm -auto
NSEQ 50
DATE Mon Jul 15 12:00:00 2013
CKSUM 8939
XT -8455 -4 0 * -8455 -4 0 *
NULT -4 -8455
NULE 595 -1558 85 338 -294 453 -1158 197 249 902 -1085 -142 -21 -313 45 531 201 384 -1998 -644
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
-104 * -3846
1 -1478 -1780 -402 -384 -1798 746 -1522 195 -1557 -1660 1115 -1800 -97 -1422 -1853 13 -1419 2556 -2187 -1765 4
P -143 -495 230 41 -385 395 124 -625 208 -465 -725 274 391 47 92 364 113 -364 -299 -254
P -1004 -1008 -9940 -2163 -365 -701 -1378 -1104 -8190
2 -3899 -3461 -5717 -754 -329 -5403 -3143 -1795 -4957 2999 -1134 -4739 -5080 -4188 -4625 -4609 -3788 -2395 3057 -1547 16
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -9 -8898 -9940 -894 -1115 -701 -1378 -8294 -8185
3 -1995 -2562 -4756 -4903 948 -2899 -4002 -4323 -4709 -4557 -3803 -3536 -3665 -4271 -4506 2845 2539 -3465 -4401 -3785 17
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -9 -8898 -9940 -894 -1115 -701 -1378 -8294 -8180
4 1974 -2894 1467 -816 -3309 781 -1179 -3058 963 -3017 -2101 -1116 189 -730 -1296 -776 170 -2597 -3194 -2516 18
D -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
D -9 -8898 -9940 -894 -1115 -701 -1378 -8294 -8175
5 1383 -2883 585 1876 -3204 405 -1043 -2954 287 -2899 -1973 -61 -2477 990 -1132 -921 -518 -602 -3067 -2384 19
A -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
A -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8170
6 -3444 -5495 2619 2744 -5608 -3223 -2646 -5588 -3024 -5423 -4830 874 -3800 1490 -3998 -3057 -3535 -5032 -5625 -4510 20
E -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
E -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8165
7 -2536 -2957 -3306 -2413 -3119 -3548 -1859 874 3060 -1039 -2114 -2413 -446 -1563 710 -2671 -2388 -2506 3242 -2796 21
K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
K -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8160
8 1087 -2878 -1251 152 -3199 57 -1039 -2949 1245 -2894 -1968 1023 -478 1653 -1127 491 694 -2500 -3062 -2379 22
N -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
N -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8155
9 998 -413 -1742 -198 -2292 -825 -1300 -1037 714 1062 420 2005 -2677 -395 -1494 -1541 -425 -661 -2537 -2029 23
K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
K -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8150
10 -3221 -2748 -5841 -5461 -3140 -5557 -5075 2551 -5338 -1071 -1986 -5198 -5343 -5155 -5383 -4856 -3201 2966 -4560 1098 24
I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
I -9 -8964 -10006 -894 -1115 -701 -1378 -8294 -8145
11 0 29 -1335 -786 -2969 -2418 -1085 -1608 1448 -65 -1823 700 -2509 1617 182 529 1205 -899 -2941 -2302 25
[Part of this file has been deleted for brevity]
F -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
F -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7340
132 -1696 -3203 2107 1686 -3513 508 -1292 -3276 -99 -3215 -2304 -545 -2698 2093 -1462 197 -974 -2821 -3384 -2676 150
E -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
E -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7331
133 -206 -3207 301 -1311 -3800 -540 -1754 -3505 3357 -3525 -2667 -1586 -3037 -1345 -1850 -1908 -2007 106 -3732 -3091 151
K -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
K -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7322
134 1654 -1721 -4245 -3631 2645 -3462 -2390 -910 -3244 1144 -791 -3131 -3508 -2856 -3053 -2564 87 891 -2223 -1892 152
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7313
135 -137 -1432 -3948 -3313 1581 -3155 -2026 -114 -2909 1428 2225 -648 -3203 -2531 -2710 -2240 -1547 1624 -1889 1109 153
M -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
M -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7304
136 1325 1101 1112 721 -3197 -363 -1036 -2947 702 -1945 -1965 -289 -2471 375 -257 1183 -1037 -2498 -3059 -2377 154
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -13 -8968 -10010 -894 -1115 -701 -1378 -8294 -7295
137 1277 -1469 -3536 -2925 -1430 1509 -1928 601 -2600 216 1186 -1524 -3132 -175 -2535 -508 -85 1083 -1920 -1568 155
M -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
M -14 -8968 -10010 -894 -1115 -701 -1378 -8294 -7285
138 -3610 -3121 -6153 -5690 1786 -5837 -5020 1076 -5518 1386 -1290 -5502 -5406 -4901 -5339 -5127 -3551 2808 -4105 -3986 156
I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
I -14 -8968 -10010 -894 -1115 -701 -1378 -8294 -7276
139 2030 2259 -3344 -2779 473 -514 -2054 -1307 -2515 -1647 -982 -2529 -3154 -2266 681 1110 -1625 881 -2225 -1864 157
C -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
C -14 -8968 -10011 -894 -1115 -701 -1378 -8294 -7267
140 502 -2761 -339 -762 -3031 -384 1988 -18 -326 -1254 -1863 1897 -2499 -629 -1172 471 1548 -2356 -2975 -2324 158
I -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
I -14 -8968 -10011 -894 -1115 -701 -1378 -8294 -7257
141 2557 -2132 1224 -2787 -2497 -3049 -2499 -1705 -2776 -586 -1671 -2638 -3386 -2536 -2949 -1127 -1982 1773 -2964 -2581 159
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -14 -8969 -10011 -894 -1115 -701 -1378 -8294 -7248
142 -4284 -3705 -6735 -6190 -2138 -6510 -5341 1840 -6011 2724 1723 -6217 -5667 -4910 -5578 -5867 -4158 115 -3948 -4121 160
L -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
L -14 -8884 -9926 -894 -1115 -701 -1378 -8294 -7238
143 1959 -2667 -1304 160 207 -440 -1064 -2658 652 -2686 -1806 -1057 -2476 -630 -1169 822 1391 -2278 -2923 -2284 161
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -14 -8825 -9867 -894 -1115 -701 -1378 -8294 -7229
144 1365 -2863 -1251 1036 -3195 -2373 3163 -2932 818 -2872 -1957 -1010 -2467 -558 298 930 -1351 -2492 -3031 -2370 162
S -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
S -14 -8825 -9868 -894 -1115 -701 -1378 -8294 -7219
145 360 -3058 -1454 144 -3448 -36 -1205 -3163 3161 -3086 -2193 -1228 -2682 -756 -274 -567 -1600 -2731 -3220 -2602 163
A -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
A -15 -8733 -9776 -894 -1115 -701 -1378 -8294 -7209
146 -5001 -4245 -5636 -5890 -650 -5388 -2113 -3919 -5374 -3258 935 -4373 -5399 -4454 -4899 -4809 -4973 -4162 -1378 4785 164
Y -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
Y -15 -8575 -9617 -894 -1115 -701 -1378 -8294 -7200
147 -3220 -3923 -3873 -2549 -201 -3790 3575 -4055 2069 -3728 -3058 -2457 -3723 -1277 2773 -3101 -2911 -3829 -3495 -3253 165
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * -8294 0
//
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> 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 |
#=AU HMMER 2.1.1 #=SQ BAHG_VITSP 1.0000 BAHG_VITSP - 0..0::0 - #=SQ GLB1_ANABR 1.0000 GLB1_ANABR - 0..0::0 - #=SQ GLB1_ARTSX 1.0000 GLB1_ARTSX - 0..0::0 - #=SQ GLB1_CALSO 1.0000 GLB1_CALSO - 0..0::0 - #=SQ GLB1_CHITH 1.0000 GLB1_CHITH - 0..0::0 - #=SQ GLB1_GLYDI 1.0000 GLB1_GLYDI - 0..0::0 - #=SQ GLB1_LUMTE 1.0000 GLB1_LUMTE - 0..0::0 - #=SQ GLB1_MORMR 1.0000 GLB1_MORMR - 0..0::0 - #=SQ GLB1_PARCH 1.0000 GLB1_PARCH - 0..0::0 - #=SQ GLB1_PETMA 1.0000 GLB1_PETMA - 0..0::0 - #=SQ GLB1_PHESE 1.0000 GLB1_PHESE - 0..0::0 - #=SQ GLB1_SCAIN 1.0000 GLB1_SCAIN - 0..0::0 - #=SQ GLB1_TYLHE 1.0000 GLB1_TYLHE - 0..0::0 - #=SQ GLB2_ANATR 1.0000 GLB2_ANATR - 0..0::0 - #=SQ GLB2_CALSO 1.0000 GLB2_CALSO - 0..0::0 - #=SQ GLB2_CHITH 1.0000 GLB2_CHITH - 0..0::0 - #=SQ GLB2_LUMTE 1.0000 GLB2_LUMTE - 0..0::0 - #=SQ GLB2_MORMR 1.0000 GLB2_MORMR - 0..0::0 - #=SQ GLB2_TYLHE 1.0000 GLB2_TYLHE - 0..0::0 - #=SQ GLB3_CHITH 1.0000 GLB3_CHITH - 0..0::0 - #=SQ GLB3_CHITP 1.0000 GLB3_CHITP - 0..0::0 - #=SQ GLB3_LAMSP 1.0000 GLB3_LAMSP - 0..0::0 - #=SQ GLB3_MORMR 1.0000 GLB3_MORMR - 0..0::0 - #=SQ GLB3_MYXGL 1.0000 GLB3_MYXGL - 0..0::0 - #=SQ GLB3_PETMA 1.0000 GLB3_PETMA - 0..0::0 - #=SQ GLB3_TYLHE 1.0000 GLB3_TYLHE - 0..0::0 - #=SQ GLB4_CHITH 1.0000 GLB4_CHITH - 0..0::0 - #=SQ GLB4_GLYDI 1.0000 GLB4_GLYDI - 0..0::0 - #=SQ GLB4_LUMTE 1.0000 GLB4_LUMTE - 0..0::0 - #=SQ GLB4_TYLHE 1.0000 GLB4_TYLHE - 0..0::0 - #=SQ GLB5_PETMA 1.0000 GLB5_PETMA - 0..0::0 - #=SQ GLB6_CHITH 1.0000 GLB6_CHITH - 0..0::0 - #=SQ GLB7_ARTSX 1.0000 GLB7_ARTSX - 0..0::0 - #=SQ GLB7_CHITH 1.0000 GLB7_CHITH - 0..0::0 - #=SQ GLB8_CHITH 1.0000 GLB8_CHITH - 0..0::0 - #=SQ GLB9_CHITH 1.0000 GLB9_CHITH - 0..0::0 - #=SQ GLBA_ANATR 1.0000 GLBA_ANATR - 0..0::0 - #=SQ GLBA_SCAIN 1.0000 GLBA_SCAIN - 0..0::0 - #=SQ GLBB_ANATR 1.0000 GLBB_ANATR - 0..0::0 - #=SQ GLBB_SCAIN 1.0000 GLBB_SCAIN - 0..0::0 - #=SQ GLBC_CAUAR 1.0000 GLBC_CAUAR - 0..0::0 - #=SQ GLBC_CHITH 1.0000 GLBC_CHITH - 0..0::0 - #=SQ GLBD_CAUAR 1.0000 GLBD_CAUAR - 0..0::0 - #=SQ GLBD_CHITH 1.0000 GLBD_CHITH - 0..0::0 - #=SQ GLBE_CHITH 1.0000 GLBE_CHITH - 0..0::0 - #=SQ GLBF_CHITH 1.0000 GLBF_CHITH - 0..0::0 - #=SQ GLBH_CHITH 1.0000 GLBH_CHITH - 0..0::0 - #=SQ GLBI_CHITP 1.0000 GLBI_CHITP - 0..0::0 - #=SQ GLBM_ANATR 1.0000 GLBM_ANATR - 0..0::0 - [Part of this file has been deleted for brevity] MYG_GALJA ................................................ MYG_GLOME ................................................ MYG_GORBE ................................................ MYG_GRAGE ................................................ MYG_HALGR ................................................ MYG_HETPO ................................................ MYG_HORSE ................................................ MYG_HUMAN ................................................ MYG_HYLAG ................................................ MYG_INIGE ................................................ MYG_KOGSI ................................................ MYG_LAGLA ................................................ MYG_LAGMA ................................................ MYG_LEPMU ................................................ MYG_LOXAF ................................................ MYG_LUTLU ................................................ MYG_LYCPI ................................................ MYG_MACFA ................................................ MYG_MACRU ................................................ MYG_MEGNO ................................................ MYG_MELME ................................................ MYG_MESCA ................................................ MYG_MOUSE ................................................ MYG_MUSAN ................................................ MYG_NYCCO ................................................ MYG_OCHPR ................................................ MYG_ORCOR ................................................ MYG_ORNAN ................................................ MYG_ORYAF ................................................ MYG_PANTR ................................................ MYG_PAPAN ................................................ MYG_PERPO ................................................ MYG_PHOPH ................................................ MYG_PHYCA ................................................ MYG_PIG ................................................ MYG_PONPY ................................................ MYG_PROGU ................................................ MYG_RABIT ................................................ MYG_ROUAE ................................................ MYG_SAISC ................................................ MYG_SHEEP ................................................ MYG_SPAEH ................................................ MYG_TACAC ................................................ MYG_THUAL ................................................ MYG_TUPGL ................................................ MYG_TURTR ................................................ MYG_VARVA ................................................ MYG_VULCH ................................................ MYG_ZALCA ................................................ MYG_ZIPCA ................................................ |
| Program name | Description |
|---|---|
| ehmmalign | Align sequences to an HMM profile |
| 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 |
| libgen | Generate discriminating elements from alignments |
| 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 |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
None