[BioRuby-cvs] bioruby/test/data/HMMER hmmpfam.out, NONE, 1.1 hmmsearch.out, NONE, 1.1
Mitsuteru C. Nakao
nakao at pub.open-bio.org
Thu Feb 2 17:11:25 UTC 2006
Update of /home/repository/bioruby/bioruby/test/data/HMMER
In directory pub.open-bio.org:/tmp/cvs-serv1957/test/data/HMMER
Added Files:
hmmpfam.out hmmsearch.out
Log Message:
* Newly added.
--- NEW FILE: hmmsearch.out ---
hmmsearch - search a sequence database with a profile HMM
HMMER 2.2g (August 2001)
Copyright (C) 1992-2001 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: /sw/share/hmmer/demo/7tm_1 [7tm_1]
Sequence database: /sw/share/hmmer/demo/P08908.fasta
per-sequence score cutoff: [none]
per-domain score cutoff: [none]
per-sequence Eval cutoff: <= 10
per-domain Eval cutoff: [none]
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Query HMM: 7tm_1
Accession: PF00001
Description: 7 transmembrane receptor (rhodopsin family)
[HMM has been calibrated; E-values are empirical estimates]
Scores for complete sequences (score includes all domains):
Sequence Description Score E-value N
-------- ----------- ----- ------- ---
sp|P08908|5H1A_HUMAN 5-hydroxytryptamine 1A receptor 377.1 5.5e-130 1
Parsed for domains:
Sequence Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
sp|P08908|5H1A_HUMAN 1/1 53 400 .. 1 275 [] 377.1 5.5e-130
Alignments of top-scoring domains:
sp|P08908|5H1A_HUMAN: domain 1 of 1, from 53 to 400: score 377.1, E = 5.5e-130
*->GNlLVilvilrtkklrtptnifilNLAvADLLflltlppwalyylvg
GN+ V+++i+++++l++++n++i++LAv+DL+++++++p+a++y v
sp|P08908| 53 GNACVVAAIALERSLQNVANYLIGSLAVTDLMVSVLVLPMAALYQVL 99
gsedWpfGsalCklvtaldvvnmyaSillLtaISiDRYlAIvhPlryrrr
+ W++G++ C+l++aldv+++++Sil+L+aI++DRY+AI++P+ y ++
sp|P08908| 100 N--KWTLGQVTCDLFIALDVLCCTSSILHLCAIALDRYWAITDPIDYVNK 147
rtsprrAkvvillvWvlalllslPpllfswvktveegngtlnvnvtvCli
rt prrA+++i+l+W++++l+s+Pp +++w++++ + +C+i
sp|P08908| 148 RT-PRRAAALISLTWLIGFLISIPP-MLGWRTPEDRSD------PDACTI 189
dfpeestasvstwlvsyvllstlvgFllPllvilvcYtrIlrtlrkrark
+ +++ y+++st+++F++Pll++lv+Y+rI+r++r r rk
sp|P08908| 190 SKDHG-----------YTIYSTFGAFYIPLLLMLVLYGRIFRAARFRIRK 228
gas...............................................
+ + ++++ +++++ ++ ++++++ ++++++++ + + +++ ++ +
sp|P08908| 229 TVKkvektgadtrhgaspapqpkksvngesgsrnwrlgveskaggalcan 278
..................................................
+ ++++++ + + ++ ++++++ + +++ ++++ + + +++++++
sp|P08908| 279 gavrqgddgaalevievhrvgnskehlplpseagptpcapasferknern 328
.....kkrsskerkaaktllvvvvvFvlCWlPyfivllldtlc.lsiims
+ ++k+ +erk++ktl++++++F+lCWlP+fiv+l+ ++c++s++m
sp|P08908| 329 aeakrKMALARERKTVKTLGIIMGTFILCWLPFFIVALVLPFCeSSCHM- 377
stCelervlptallvtlwLayvNsclNPiIY<-*
+ + +++wL+y+Ns lNP+IY
sp|P08908| 378 --------PTLLGAIINWLGYSNSLLNPVIY 400
Histogram of all scores:
score obs exp (one = represents 1 sequences)
----- --- ---
377 1 0|=
% Statistical details of theoretical EVD fit:
mu = -10.6639
lambda = 0.7676
chi-sq statistic = 0.0000
P(chi-square) = 0
Total sequences searched: 1
Whole sequence top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 16K
Domain top hits:
tophits_s report:
Total hits: 1
Satisfying E cutoff: 1
Total memory: 17K
--- NEW FILE: hmmpfam.out ---
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: /Users/nakao/Sites/iprscan/data/Pfam
Sequence file: /Users/nakao/Sites/iprscan/tmp/20050517/iprscan-20050517-16244071/chunk_1/iprscan-20050517-16244071.nocrc
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Query sequence: 104K_THEPA
Accession: [none]
Description: [none]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
PF04385.4 Domain of unknown function, DUF529 259.3 6.6e-75 4
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
PF04385.4 1/4 36 111 .. 1 80 [] 65.0 2e-16
PF04385.4 2/4 149 224 .. 1 80 [] 64.7 2.5e-16
PF04385.4 3/4 265 343 .. 1 80 [] 64.6 2.7e-16
PF04385.4 4/4 379 456 .. 1 80 [] 65.0 2e-16
Alignments of top-scoring domains:
PF04385.4: domain 1 of 4, from 36 to 111: score 65.0, E = 2e-16
*->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
t+D+n++++ f +v+++g+++ + ++ ++v+++++++Gn+v+W
104K_THEPA 36 TFDINSNQTG-PAFLTAVEMAGVKYLQVQHGSNVNIHRLVEGNVVIW 81
eseddpefglivtlsfyldsnkfLvlllintak<-*
e++ + +l++ ++++++++++++++++ +++
104K_THEPA 82 ENA---STPLYTGAIVTNNDGPYMAYVEVLGDP 111
PF04385.4: domain 2 of 4, from 149 to 224: score 64.7, E = 2.5e-16
*->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+L++ ++ +++k+ + ++a+ng ++vt++p++G+ +++++++n++++
104K_THEPA 149 SLNMAFQLENNKYEVETHAKNGANMVTFIPRNGHICKMVYHKNVRIY 195
eseddpefglivtlsfyldsnkfLvlllintak<-*
++ ++++vt++++++ +++L+l+++ +
104K_THEPA 196 KA----TGNDTVTSVVGFFRGLRLLLINVFSID 224
PF04385.4: domain 3 of 4, from 265 to 343: score 64.6, E = 2.7e-16
*->tLDlndtgstlkqfdykvalngdivvtytpkpGvkftkitdGnevvW
+Dl+ +++ +++f+ + a+++ ++++++p++G+++tk++dG++v++
104K_THEPA 265 PVDLDIKDIDYTMFHLADATYHEPCFKIIPNTGFCITKLFDGDQVLY 311
eseddpefglivtlsfyldsnkfLvlllintak<-*
es+ + + ++i +++y+++n ++++l++n+++
104K_THEPA 312 ESFNP-LIHCINEVHIYDRNNGSIICLHLNYSP 343
PF04385.4: domain 4 of 4, from 379 to 456: score 65.0, E = 2e-16
*->tLDlndtgstlkqfdykvalngdivvty.tpkpGvkftkitdGnevv
+LD+n ++++k+ +++ +n d +t+ tp+p+ + +++dG+ev+
104K_THEPA 379 ELDVN--FISDKDLYVAALTNADLNYTMvTPRPHRDVIRVSDGSEVL 423
WeseddpefglivtlsfyldsnkfLvlllintak<-*
W++e+ ++ l++++++++d++ +Lv+l+i++
104K_THEPA 424 WYYEGL-DNFLVCAWIYVSDGVASLVHLRIKDRI 456
//
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