ehmmpfam |
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Usage:
ehmmpfam [options] hmmfile seqfile outfile
The outfile parameter is new to EMBASSY HMMER.
hmmpfam reads a sequence file
Go to the input files for this example
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).
ehmmpfam reads any normal sequence USAs.
The following additional options are provided:
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.
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.
Jon Ison
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.
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 ehmmpfam
% ehmmpfam ../ehmmcalibrate-ex2-keep/myhmmso 7LES_DROME myhmmso.ehmmpfam -A 10 -E 10
Search one or more sequences against an HMM database.
/shared/software/bin/hmmpfam -A 10 -E 10.000000 -T -1000000.000000 -Z 59021 --domE 1000000.000000 --domT -1000000.000000 --informat FASTA ../ehmmcalibrate-ex2-keep/myhmmso ./ehmmpfam-1234567890.1234
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.
Search one or more sequences against an HMM database.
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-hmmfile] infile File of HMMs.
[-seqfile] seqall File of sequences.
-a integer [100] Limits the alignment output to the
Qualifier
Type
Description
Allowed values
Default
Standard (Mandatory) qualifiers
[-hmmfile]
(Parameter 1)infile
File of HMMs.
Input file
Required
[-seqfile]
(Parameter 2)seqall
File of sequences.
Readable sequence(s)
Required
-a
integer
Limits the alignment output to the <n> best scoring domains. -A0 shuts off the alignment output and can be used to reduce the size of output files.
Any integer value
100
-e
float
Set the E-value cutoff for the per-sequence ranked hit list to <x>, where <x> is a positive real number. The default is 10.0. Hits with E-values better than (less than) this threshold will be shown.
Any numeric value
10.
[-outfile]
(Parameter 3)outfile
There is a separate output report for each sequence in seqfile. This report consists of three sections: a ranked list of the best scoring HMMs, a list of the best scoring domains in order of their occurrence in the sequence, and alignments for all the best scoring domains.
Output file
<*>.ehmmpfam
Additional (Optional) qualifiers
-nuc
boolean
Specify that models and sequence are nucleic acid, not protein. Other HMMER programs autodetect this; but because of the order in which hmmpfam accesses data, it can't reliably determine the correct 'alphabet' by itself.
Boolean value Yes/No
No
-t
float
Set the bit score cutoff for the per-sequence ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, the threshold is controlled by E-value and not by bit score. Hits with bit scores better than (greater than) this threshold will be shown.
Any numeric value
-1000000.
-z
integer
Calculate the E-value scores as if we had seen a sequence database of <n> sequences. The default is arbitrarily set to 59021, the size of Swissprot 34.
Any integer value
59021
Advanced (Unprompted) qualifiers
-acc
boolean
Report HMM accessions instead of names in the output reports. Useful for high-throughput annotation, where the data are being parsed for storage in a relational database.
Boolean value Yes/No
No
-compat
boolean
Use the output format of HMMER 2.1.1, the 1998-2001 public release; provided so 2.1.1 parsers don't have to be rewritten.
Boolean value Yes/No
No
-cpu
integer
Sets the maximum number of CPUs that the program will run on. The default is to use all CPUs in the machine. Overrides the HMMER NCPU environment variable. Only affects threaded versions of HMMER (the default on most systems).
Any integer value
0
-cutga
boolean
Use Pfam GA (gathering threshold) score cutoffs. Equivalent to -globT <GA1> -domT <GA2>, but the GA1 and GA2 cutoffs are read from each HMM in the input HMM database individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional GA annotation line was present. If these cutoffs are not set in the HMM file, -cut ga doesn't work.
Boolean value Yes/No
No
-cuttc
boolean
Use Pfam TC (trusted cutoff) score cutoffs. Equivalent to -globT <TC1> -domT <TC2>, but the TC1 and TC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional TC annotation line was present. If these cutoffs are not set in the HMM file, -cut tc doesn't work.
Boolean value Yes/No
No
-cutnc
boolean
Use Pfam NC (noise cutoff) score cutoffs. Equivalent to -globT <NC1> -domT <NC2>, but the NC1 and NC2 cutoffs are read from each HMM in hmmfile individually. hmmbuild puts these cutoffs there if the alignment file was annotated in a Pfam-friendly alignment format (extended SELEX or Stockholm format) and the optional NC annotation line was present. If these cutoffs are not set in the HMM file, -cut nc doesn't work.
Boolean value Yes/No
No
-dome
float
Set the E-value cutoff for the per-domain ranked hit list to <x>, where <x> is a positive real number. The default is infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list.
Any numeric value
1000000.
-domt
float
Set the bit score cutoff for the per-domain ranked hit list to <x>, where <x> is a real number. The default is negative infinity; by default, all domains in the sequences that passed the frst threshold will be reported in the second list, so that the number of domains reported in the per-sequence list is consistent with the number that appear in the per-domain list. Important note: only one domain in a sequence is absolutely controlled by this parameter, or by --domT. The second and subsequent domains in a sequence have a de facto bit score threshold of 0 because of the details of how HMMER works. HMMER requires at least one pass through the main model per sequence; to do more than one pass (more than one domain) the multidomain alignment must have a better score than the single domain alignment, and hence the extra domains must contribute positive score. See the Users' Guide for more detail.
Any numeric value
-1000000.
-forward
boolean
Use the Forward algorithm instead of the Viterbi algorithm to determine the per-sequence scores. Per-domain scores are still determined by the Viterbi algorithm. Some have argued that Forward is a more sensitive algorithm for detecting remote sequence homologues; my experiments with HMMER have not confrmed this, however.
Boolean value Yes/No
No
-nulltwo
boolean
Turn off the post hoc second null model. By default, each alignment is rescored by a postprocessing step that takes into account possible biased composition in either the HMM or the target sequence. This is almost essential in database searches, especially with local alignment models. There is a very small chance that this postprocessing might remove real matches, and in these cases --null2 may improve sensitivity at the expense of reducing specifcity by letting biased composition hits through.
Boolean value Yes/No
No
-pvm
boolean
Run on a Parallel Virtual Machine (PVM). The PVM must already be running. The client program hmmpfam-pvm must be installed on all the PVM nodes. The HMM database hmmfile and an associated GSI index file hmmfile.gsi must also be installed on all the PVM nodes. (The GSI index is produced by the program hmmindex.) Because the PVM implementation is I/O bound, it is highly recommended that each node have a local copy of hmmfile rather than NFS mounting a shared copy. Optional PVM support must have been compiled into HMMER for -pvm to function.
Boolean value Yes/No
No
-xnu
boolean
Turn on XNU filtering of target protein sequences. Has no effect on nucleic acid sequences. In trial experiments, -xnu appears to perform less well than the default post hoc null2 model.
Boolean value Yes/No
No
Associated qualifiers
"-seqfile" associated seqall qualifiers
-sbegin2
-sbegin_seqfileinteger
Start of each sequence to be used
Any integer value
0
-send2
-send_seqfileinteger
End of each sequence to be used
Any integer value
0
-sreverse2
-sreverse_seqfileboolean
Reverse (if DNA)
Boolean value Yes/No
N
-sask2
-sask_seqfileboolean
Ask for begin/end/reverse
Boolean value Yes/No
N
-snucleotide2
-snucleotide_seqfileboolean
Sequence is nucleotide
Boolean value Yes/No
N
-sprotein2
-sprotein_seqfileboolean
Sequence is protein
Boolean value Yes/No
N
-slower2
-slower_seqfileboolean
Make lower case
Boolean value Yes/No
N
-supper2
-supper_seqfileboolean
Make upper case
Boolean value Yes/No
N
-sformat2
-sformat_seqfilestring
Input sequence format
Any string
-sdbname2
-sdbname_seqfilestring
Database name
Any string
-sid2
-sid_seqfilestring
Entryname
Any string
-ufo2
-ufo_seqfilestring
UFO features
Any string
-fformat2
-fformat_seqfilestring
Features format
Any string
-fopenfile2
-fopenfile_seqfilestring
Features file name
Any string
"-outfile" associated outfile qualifiers
-odirectory3
-odirectory_outfilestring
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
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.
Input files for usage example
File: ../ehmmcalibrate-ex2-keep/myhmmso
HMMER2.0 [2.3.2]
NAME rrm
LENG 77
ALPH Amino
RF no
CS no
MAP yes
COM /shared/software/bin/hmmbuild -n rrm --pbswitch 1000 --archpri 0.850000 --idlevel 0.620000 --swentry 0.500000 --swexit 0.500000 --wgsc -A -F myhmms ../../data/hmmnew/rrm.sto
COM /shared/software/bin/hmmcalibrate --mean 350.000000 --num 5000 --sd 350.000000 --seed 1 ../ehmmbuild-ex4-keep/myhmms
NSEQ 90
DATE Fri Jul 15 12:00:00 2011
CKSUM 8325
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 -45.860321 0.213107
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
-16 * -6492
1 -1084 390 -8597 -8255 -5793 -8424 -8268 2395 -8202 2081 -1197 -8080 -8115 -8020 -8297 -7789 -5911 1827 -7525 -7140 1
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 -16 *
2 -2140 -3785 -6293 -2251 3226 -2495 -727 -638 -2421 -545 -675 -5146 -5554 -4879 -1183 -2536 -1928 267 76 3171 2
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
3 -2542 458 -8584 -8273 -6055 -8452 -8531 2304 -8255 -324 101 -8104 -8170 -8221 -8440 -7840 -5878 3145 -7857 -7333 3
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
4 -1505 -5144 -1922 -558 -1842 2472 -3303 -2213 1099 -5160 -4233 372 -4738 -530 1147 168 498 -4766 -5327 -1476 4
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
5 -3724 -5184 300 -3013 -1655 1803 -3353 -5245 -1569 -2686 -4276 3495 -1963 -1331 -1054 -1472 -3664 -4803 -5369 -2 5
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
6 -1569 -6106 -8967 -8363 555 -8531 -7279 654 -8092 2953 -94 -8220 -7908 -1643 -7682 -7771 -6460 -59 -6191 -6284 6
- -151 -504 230 45 -380 399 101 -621 211 -470 -713 278 399 48 91 360 113 -364 -299 -254
- -178 -3113 -12684 -1600 -578 -701 -1378 * *
7 -409 -5130 -215 -2987 -1709 -956 690 -5188 -395 -5144 -4224 729 3054 -2862 -3409 354 1293 -1381 -5321 -4644 13
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
8 -3674 -5118 -1004 639 420 -4652 176 -2050 404 -1039 -935 16 1755 168 147 -275 198 -1472 1889 1977 14
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
9 -408 -5134 2415 1299 -950 -66 -767 -1296 -2889 -1843 -4224 1084 -968 -1439 -1854 540 -314 -2304 -5320 -60 15
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
10 586 1804 -6294 -631 -1627 -1671 -4374 1029 -2223 -162 1172 -5147 -5554 -1870 -5058 -2327 1741 1687 -4242 687 16
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11642 -12684 -894 -1115 -701 -1378 * *
11 -2134 -5144 845 -1187 -1652 -1667 -3303 -5216 -513 -801 -4233 1026 -1873 -543 -619 575 2956 -4766 -5327 -4644 17
[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
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
279 -7207 -7306 -8076 -6588 -8459 -7223 -5448 -7982 -1500 -7531 -6953 -6369 -7277 -5081 4236 -7139 -6862 -7777 -7053 -7277 454
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
280 -694 -163 -5922 -5286 -1204 -2048 -610 1082 -1800 1434 -2618 -4776 2951 -4509 -4688 -1216 -1648 -2829 202 21 455
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -3168 -11253 -171 -894 -1115 -701 -1378 * *
281 -1412 -2132 -2007 -2293 -4366 3113 -2847 -4225 -3107 -4377 -3503 1660 -2881 -2661 -3396 961 -1821 -3134 -4516 -4119 456
- -150 -489 232 42 -382 400 104 -627 211 -465 -722 274 393 51 95 359 116 -370 -296 -245
- -2121 -637 -2975 -831 -1191 -6099 -21 * *
282 -968 -1818 -1787 -1351 -3112 953 -1494 -2818 -1122 -2911 -2044 -1365 -2340 -1133 1510 1816 2121 -2205 -3137 -2649 459
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -228 -7899 -2816 -894 -1115 -4964 -47 * *
283 840 -1663 -994 969 1159 503 -604 -1413 -325 -1594 -814 -688 -1996 -267 1103 -851 -755 -1179 2900 -1437 460
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -9 -7938 -8980 -894 -1115 -89 -4060 * *
284 -3257 -4642 -697 -2590 -1218 -252 -2907 -4655 -1306 -2353 -529 482 -1607 -2459 -1398 2112 2745 -4246 -4848 -4187 461
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11183 -12226 -894 -1115 -186 -3045 * *
285 2163 763 -1619 -5296 2250 -2060 -4007 1241 -4891 -489 484 -4781 -226 -4515 -4692 -678 -1688 -813 264 -3530 462
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
286 -268 -329 -158 917 -541 -1990 350 -4851 1273 -1075 388 -1130 233 840 993 -602 801 -595 -4964 -857 463
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
287 109 -243 672 2304 -5103 -4283 488 -4854 -1317 -2269 -656 -492 -1519 2679 -655 -618 -3248 -4404 -4965 -1114 464
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
288 1312 1294 -6215 -5593 -206 -1244 -4339 2188 -5201 1409 395 -5091 -5478 -4828 -5009 -4538 -3794 1162 -4187 -3846 465
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -23 -11253 -6022 -894 -1115 -701 -1378 * *
289 -3562 799 -5767 -2054 -1235 -2075 318 138 237 2164 1713 -1454 -5145 -1272 -730 -4172 -1640 1071 -3865 -34 466
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -1470 -646 * *
290 73 1351 -674 1236 -1549 -2008 1350 -4834 1049 -2498 -3851 1801 -4356 1813 -115 -223 -1582 -1052 -4945 -4262 467
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11231 -12273 -894 -1115 -369 -2147 * *
291 -1739 -320 777 -2654 -1419 -2051 4360 -4707 -1358 -2412 -689 -1300 -4399 -224 537 531 -289 -2010 -4905 -1057 468
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -11253 -12295 -894 -1115 -701 -1378 * *
292 -3345 -4494 -233 -332 -563 -1986 -3051 333 99 1063 -3616 -3072 2953 -1026 -1490 -943 -1528 -1070 -4753 -4151 469
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10815 -11857 -894 -1115 -701 -1378 * *
293 -6409 -5751 -7614 -7636 2593 -7311 -4003 -5084 -7219 -150 -151 -6210 -7172 -849 -6723 -6510 -6299 -1387 4881 2807 470
- -149 -500 233 43 -381 399 106 -626 210 -466 -720 275 394 45 96 359 117 -369 -294 -249
- -1 -10749 -11791 -894 -1115 -701 -1378 * *
294 -4057 -3817 -6415 -5791 3203 -1638 -4541 1679 -5412 765 1434 -5333 -5617 -4930 -5182 -4791 -3987 1226 750 -3959 471
- * * * * * * * * * * * * * * * * * * * *
- * * * * * * * * 0
//
File: 7LES_DROME
ID 7LES_DROME STANDARD; PRT; 2554 AA.
AC P13368;
DT 01-JAN-1990 (Rel. 13, Created)
DT 01-JAN-1990 (Rel. 13, Last sequence update)
DT 01-NOV-1997 (Rel. 35, Last annotation update)
DE SEVENLESS PROTEIN (EC 2.7.1.112).
GN SEV.
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Arthropoda; Tracheata; Hexapoda; Insecta;
OC Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC Ephydroidea; Drosophilidae; Drosophila.
RN [1]
RP SEQUENCE FROM N.A.
RC STRAIN=CANTON-S;
RX MEDLINE; 88282538.
RA BASLER K., HAFEN E.;
RT "Control of photoreceptor cell fate by the sevenless protein requires
RT a functional tyrosine kinase domain.";
RL Cell 54:299-311(1988).
RN [2]
RP SEQUENCE FROM N.A.
RC STRAIN=OREGON-R;
RX MEDLINE; 88329706.
RA BOWTELL D.L.L., SIMON M.A., RUBIN G.M.;
RT "Nucleotide sequence and structure of the sevenless gene of
RT Drosophila melanogaster.";
RL Genes Dev. 2:620-634(1988).
RN [3]
RP IDENTIFICATION OF FN-III REPEATS.
RX MEDLINE; 90199889.
RA NORTON P.A., HYNES R.O., RESS D.J.G.;
RT "Sevenless: seven found?";
RL Cell 61:15-16(1990).
CC -!- FUNCTION: RECEPTOR FOR AN EXTRACELLULAR SIGNAL REQUIRED TO
CC INSTRUCT A CELL TO DIFFERENTIATE INTO A R7 PHOTORECEPTOR. THE
CC LIGAND FOR SEV IS THE BOSS (BRIDE OF SEVENLESS) PROTEIN ON THE
CC SURFACE OF THE NEIGHBORING R8 CELL.
CC -!- CATALYTIC ACTIVITY: ATP + A PROTEIN TYROSINE = ADP +
CC PROTEIN TYROSINE PHOSPHATE.
CC -!- SUBUNIT: MAY FORM A COMPLEX WITH DRK AND SOS.
CC -!- SIMILARITY: BELONGS TO THE INSULIN RECEPTOR FAMILY OF TYROSINE-
CC PROTEIN KINASES. SEVENLESS SUBFAMILY.
CC -!- SIMILARITY: CONTAINS 7 FIBRONECTIN TYPE III-LIKE DOMAINS.
CC -!- CAUTION: UNCLEAR WHETHER THE POTENTIAL MEMBRANE SPANNING REGION
CC NEAR THE N-TERMINUS IS PRESENT AS A TRANSMEMBRANE DOMAIN IN THE
CC NATIVE PROTEIN OR SERVES AS A CLEAVED SIGNAL SEQUENCE.
CC --------------------------------------------------------------------------
CC This SWISS-PROT entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
[Part of this file has been deleted for brevity]
FT VARIANT 1703 1703 N -> H.
FT VARIANT 1730 1730 R -> K.
FT VARIANT 1731 1731 G -> E.
FT VARIANT 1741 1741 V -> M.
FT VARIANT 2271 2271 R -> C.
FT CONFLICT 1823 1823 E -> Q (IN REF. 2).
SQ SEQUENCE 2554 AA; 287107 MW; 1143D891 CRC32;
MTMFWQQNVD HQSDEQDKQA KGAAPTKRLN ISFNVKIAVN VNTKMTTTHI NQQAPGTSSS
SSNSQNASPS KIVVRQQSSS FDLRQQLARL GRQLASGQDG HGGISTILII NLLLLILLSI
CCDVCRSHNY TVHQSPEPVS KDQMRLLRPK LDSDVVEKVA IWHKHAAAAP PSIVEGIAIS
SRPQSTMAHH PDDRDRDRDP SEEQHGVDER MVLERVTRDC VQRCIVEEDL FLDEFGIQCE
KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL
QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE
LDLEQEDQDA SGETGSSAWF NLADYDCDEY YMCEILEALI PYTQYRFRFE LPFGENRDEV
LYSPATPAYQ TPPEGAPISA PVIEHLMGLD DSHLAVHWHP GRFTNGPIEG YRLRLSSSEG
NATSEQLVPA GRGSYIFSQL QAGTNYTLAL SMINKQGEGP VAKGFVQTHS ARNEKPAKDL
TESVLLVGRR AVMWQSLEPA GENSMIYQSQ EELADIAWSK REQQLWLLNV HGELRSLKFE
SGQMVSPAQQ LKLDLGNISS GRWVPRRLSF DWLHHRLYFA MESPERNQSS FQIISTDLLG
ESAQKVGESF DLPVEQLEVD ALNGWIFWRN EESLWRQDLH GRMIHRLLRI RQPGWFLVQP
QHFIIHLMLP QEGKFLEISY DGGFKHPLPL PPPSNGAGNG PASSHWQSFA LLGRSLLLPD
SGQLILVEQQ GQAASPSASW PLKNLPDCWA VILLVPESQP LTSAGGKPHS LKALLGAQAA
KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR
VRAINVDGEP GEWTEPLAAR TWPLGPHRLR WASRQGSVIH TNELGEGLEV QQEQLERLPG
PMTMVNESVG YYVTGDGLLH CINLVHSQWG CPISEPLQHV GSVTYDWRGG RVYWTDLARN
CVVRMDPWSG SRELLPVFEA NFLALDPRQG HLYYATSSQL SRHGSTPDEA VTYYRVNGLE
GSIASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR
PLGALLWLER SGRRARLVRL AAPLDVMELP TPDQASPASA LQLLDPQPLP PRDEGVIPMT
VLPDSVRLDD GHWDDFHVRW QPSTSGGNHS VSYRLLLEFG QRLQTLDLST PFARLTQLPQ
AQLQLKISIT PRTAWRSGDT TRVQLTTPPV APSQPRRLRV FVERLATALQ EANVSAVLRW
DAPEQGQEAP MQALEYHISC WVGSELHEEL RLNQSALEAR VEHLQPDQTY HFQVEARVAA
TGAAAGAASH ALHVAPEVQA VPRVLYANAE FIGELDLDTR NRRRLVHTAS PVEHLVGIEG
EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY
RLDLCNFEGK ILQGERVWST PRGRLLKDLV ALPQAQSLIW LEYEQGSPRN GSLRGRNLTD
GSELEWATVQ PLIRLHAGSL EPGSETLNLV DNQGKLCVYD VARQLCTASA LRAQLNLLGE
DSIAGQLAQD SGYLYAVKNW SIRAYGRRRQ QLEYTVELEP EEVRLLQAHN YQAYPPKNCL
LLPSSGGSLL KATDCEEQRC LLNLPMITAS EDCPLPIPGV RYQLNLTLAR GPGSEEHDHG
VEPLGQWLLG AGESLNLTDL LPFTRYRVSG ILSSFYQKKL ALPTLVLAPL ELLTASATPS
PPRNFSVRVL SPRELEVSWL PPEQLRSESV YYTLHWQQEL DGENVQDRRE WEAHERRLET
AGTHRLTGIK PGSGYSLWVQ AHATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA
GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RYQCRLLLGY AATPGAPLYH
GTAEVYETLG DAPSQPGKPQ LEHIAEEVFR VTWTAARGNG APIALYNLEA LQARSDIRRR
RRRRRRNSGG SLEQLPWAEE PVVVEDQWLD FCNTTELSCI VKSLHSSRLL LFRVRARSLE
HGWGPYSEES ERVAEPFVSP EKRGSLVLAI IAPAAIVSSC VLALVLVRKV QKRRLRAKKL
LQQSRPSIWS NLSTLQTQQQ LMAVRNRAFS TTLSDADIAL LPQINWSQLK LLRFLGSGAF
GEVYEGQLKT EDSEEPQRVA IKSLRKGASE FAELLQEAQL MSNFKHENIV RLVGICFDTE
SISLIMEHME AGDLLSYLRA ARATSTQEPQ PTAGLSLSEL LAMCIDVANG CSYLEDMHFV
HRDLACRNCL VTESTGSTDR RRTVKIGDFG LARDIYKSDY YRKEGEGLLP VRWMSPESLV
DGLFTTQSDV WAFGVLCWEI LTLGQQPYAA RNNFEVLAHV KEGGRLQQPP MCTEKLYSLL
LLCWRTDPWE RPSFRRCYNT LHAISTDLRR TQMASATADT VVSCSRPEFK VRFDGQPLEE
HREHNERPED ENLTLREVPL KDKQLYANEG VSRL
//
Output file format
ehmmpfam
outputs a graph to the specified graphics device.
outputs a report format file. The default format is ...
Output files for usage example
File: myhmmso.ehmmpfam
hmmpfam - search one or more sequences against HMM database
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-ex2-keep/myhmmso
Sequence file: ./ehmmpfam-1234567890.1234
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query sequence: 7LES_DROME
Accession: [none]
Description: P13368 SEVENLESS PROTEIN (EC 2.7.1.112).
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
pkinase Protein kinase domain 314.6 1.2e-90 1
fn3 Fibronectin type III domain 176.6 4e-49 6
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
fn3 1/6 437 522 .. 1 84 [] 48.3 1.7e-10
fn3 2/6 825 914 .. 1 84 [] 13.4 0.09
fn3 3/6 1292 1389 .. 1 84 [] 15.9 0.05
fn3 4/6 1799 1891 .. 1 84 [] 63.5 4.5e-15
fn3 5/6 1899 1978 .. 1 84 [] 15.2 0.06
fn3 6/6 1993 2107 .. 1 84 [] 20.3 0.018
pkinase 1/1 2209 2483 .. 1 294 [] 314.6 1.2e-90
Alignments of top-scoring domains:
fn3: domain 1 of 6, from 437 to 522: score 48.3, E = 1.7e-10
CS C CCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
*->P.saPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge
P saP + +++ ++ l ++W p + ngpi+gY++++ +++ g+
7LES_DROME 437 PiSAPVIEHLMGLDDSHLAVHWHPGRfTNGPIEGYRLRL-SSSEGNA 482
CS CCCCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
wneltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
+ e+ vp sy+++ L++gt+Y++ + +n +G+Gp
7LES_DROME 483 TSEQLVPAGRGSYIFSQLQAGTNYTLALSMINKQGeGPVA 522
fn3: domain 2 of 6, from 825 to 914: score 13.4, E = 0.09
CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.EC
*->PsaPtnltvtdvtstsltlsWsppt.......gngpitgYevtyRqp
++P l++ ++ + +sW+ p++++ ++ + + +Ye+++ +
7LES_DROME 825 GGKPHSLKALL-GAQAAKISWKEPErnpyqsaDAARSWSYELEV-LD 869
CS CCCCCCCCCE EECCCCCECECCEEEEECCCCEEEEEECCC CCCC
knggewnelt.vpgtttsytltgLkPgteYevrVqAvnggG..GpeS<-*
[Part of this file has been deleted for brevity]
CS CCEEECCCCCECECCEEEEECCCCEEEEEECCC CCCC
eltvpgtttsytltgLkPgteYevrVqAvnggG.GpeS<-*
+++v g+ t ++++ L+P t+Y+ r+ ++++G++
7LES_DROME 1941 RRNVAGNHTKMVVEPLQPRTRYQCRLLLGYAATpGAPL 1978
fn3: domain 6 of 6, from 1993 to 2107: score 20.3, E = 0.018
CS CCCCCEEEEEECCTTCCEEEEECCC CCCCCCCEEEEE.ECCCCCC
*->PsaPtnltvtdvtstsltlsWsppt.gngpitgYevtyRqpkngge.
Ps+P+ ++ + + + ++++W++++++++pi Y+++ ++++ +
7LES_DROME 1993 PSQPGKPQLEHIAEEVFRVTWTAARgNGAPIALYNLEA-LQARSDIr 2038
CS CCCCEEECCCC CECECCEEEEE
...........................wneltvpgttt.sytltgLkPgt
+++++++++++++ ++ + +++ ++++l+ +tt s++++ L +
7LES_DROME 2039 rrrrrrrrnsggsleqlpwaeepvvveDQWLDFCNTTElSCIVKSLHSSR 2088
CS CCCCEEEEEE CCC CCCC
eYevrVqAvn.ggG.GpeS<-*
+rV+A++ ++G Gp+S
7LES_DROME 2089 LLLFRVRARSlEHGwGPYS 2107
pkinase: domain 1 of 1, from 2209 to 2483: score 314.6, E = 1.2e-90
*->yelleklGeGsfGkVykakhkd...ktgkiVAvKilkkekesikekr
++ll+ lG+G+fG+Vy++++k+++++ ++VA+K l+k+++++ e
7LES_DROME 2209 LKLLRFLGSGAFGEVYEGQLKTedsEEPQRVAIKSLRKGASEFAE-- 2253
flrEiqilkrLsHpNIvrligvfedtddhlylvmEymegGdLfdylrrng
+l E+q++ +++H+NIvrl g++ + +++ l+mE+me GdL++ylr+ +
7LES_DROME 2254 LLQEAQLMSNFKHENIVRLVGICF-DTESISLIMEHMEAGDLLSYLRAAR 2302
..........gplsekeakkialQilrGleYLHsngivHRDLKpeNILld
+++++++++ ls e++ ++ ++++G +YL+++++vHRDL+ +N+L++
7LES_DROME 2303 atstqepqptAGLSLSELLAMCIDVANGCSYLEDMHFVHRDLACRNCLVT 2352
en......dgtvKiaDFGLArlle..sssklttfvGTpwYmmAPEvileg
e +++++++ tvKi+DFGLAr++++++++++ + + p+++m+PE l +
7LES_DROME 2353 EStgstdrRRTVKIGDFGLARDIYksDYYRKEGEGLLPVRWMSPES-LVD 2401
rgysskvDvWSlGviLyElltggplfpgadlpaftggdevdqliifvlkl
+++++DvW++Gv+++E+lt g ++
7LES_DROME 2402 GLFTTQSDVWAFGVLCWEILTLG-------------------------QQ 2426
PfsdelpktridpleelfriikrpglrlplpsncSeelkdLlkkcLnkDP
P+ ++ +e+++++k+ g+rl +p+ c e l++Ll c++ DP
7LES_DROME 2427 PYAA-------RNNFEVLAHVKE-GGRLQQPPMCTEKLYSLLLLCWRTDP 2468
skRpGsatakeilnhpwf<-*
++Rp +++ + n +
7LES_DROME 2469 WERP---SFRRCYNTLHA 2483
//
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.
-n : Use -nuc instead (-n causes problems for GUI developers)
-outfile : Output file with HMM.
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.
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 with Environment 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
Disk space requirements
ehmmpfam makes a temporary local copy of its input sequence data. You must ensure there is sufficient disk space for this in the directory that ehmmpfam is run.
Diagnostic Error Messages
None.
Exit status
It always exits with status 0.
Known bugs
None.
See also
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
ehmmsearch
Search a sequence database with a profile HMM
libgen
Generate discriminating elements from alignments
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.
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
History
Target users
This program is intended to be used by everyone and everything, from naive users to embedded scripts.