ngoto-bio 1.2.9.9001

data/test/data/HMMER/hmmpfam.out

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+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
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+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  
+
+//

data/test/data/HMMER/hmmsearch.out

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+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)
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+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]
+- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+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

data/test/data/SOSUI/sample.report

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+>Q9HC19
+ MEMBRANE PROTEIN
+ NUMBER OF TM HELIX = 7
+ TM 1   31-  53 SECONDARY   HIRMTFLRKVYSILSLQVLLTTV
+ TM 2   69-  90 PRIMARY     HESPALILLFALGSLGLIFALT
+ TM 3   99- 121 PRIMARY     NLYLLFGFTLLEALTVAVVVTFY
+ TM 4  124- 146 PRIMARY     YIILQAFILTTTVFFGLTVYTLQ
+ TM 5  153- 175 PRIMARY     KFGAGLFALLWILCLSGILEVFF
+ TM 6  181- 203 PRIMARY     ELVLAAAGALLFCGFIIYDTHSL
+ TM 7  212- 234 SECONDARY   YVLAAISLYLDIINLFLHLLRFL
+

data/test/data/TMHMM/sample.report

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+# O42385 Length: 423
+# O42385 Number of predicted TMHs:  7
+# O42385 Exp number of AAs in TMHs: 157.40784
+# O42385 Exp number, first 60 AAs:  13.85627
+# O42385 Total prob of N-in:        0.00993
+# O42385 POSSIBLE N-term signal sequence
+O42385  TMHMM2.0        outside      1    46
+O42385  TMHMM2.0        TMhelix     47    69
+O42385  TMHMM2.0        inside      70    81
+O42385  TMHMM2.0        TMhelix     82   104
+O42385  TMHMM2.0        outside    105   118
+O42385  TMHMM2.0        TMhelix    119   141
+O42385  TMHMM2.0        inside     142   161
+O42385  TMHMM2.0        TMhelix    162   184
+O42385  TMHMM2.0        outside    185   205
+O42385  TMHMM2.0        TMhelix    206   228
+O42385  TMHMM2.0        inside     229   348
+O42385  TMHMM2.0        TMhelix    349   371
+O42385  TMHMM2.0        outside    372   380
+O42385  TMHMM2.0        TMhelix    381   403
+O42385  TMHMM2.0        inside     404   423

data/test/data/aaindex/DAYM780301

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+H DAYM780301
+D Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
+R
+A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
+T A model of evolutionary change in proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff,
+  M.O., ed.), National Biomedical Research Foundation, Washington, D.C.,
+  p.352 (1978)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+      2.
+     -2.      6.
+      0.      0.      2.
+      0.     -1.      2.      4.
+     -2.     -4.     -4.     -5.     12.
+      0.      1.      1.      2.     -5.      4.
+      0.     -1.      1.      3.     -5.      2.      4.
+      1.     -3.      0.      1.     -3.     -1.      0.      5.
+     -1.      2.      2.      1.     -3.      3.      1.     -2.      6.
+     -1.     -2.     -2.     -2.     -2.     -2.     -2.     -3.     -2.      5.
+     -2.     -3.     -3.     -4.     -6.     -2.     -3.     -4.     -2.      2.      6.
+     -1.      3.      1.      0.     -5.      1.      0.     -2.      0.     -2.     -3.      5.
+     -1.      0.     -2.     -3.     -5.     -1.     -2.     -3.     -2.      2.      4.      0.      6.
+     -4.     -4.     -4.     -6.     -4.     -5.     -5.     -5.     -2.      1.      2.     -5.      0.      9.
+      1.      0.     -1.     -1.     -3.      0.     -1.     -1.      0.     -2.     -3.     -1.     -2.     -5.      6.
+      1.      0.      1.      0.      0.     -1.      0.      1.     -1.     -1.     -3.      0.     -2.     -3.      1.      2.
+      1.     -1.      0.      0.     -2.     -1.      0.      0.     -1.      0.     -2.      0.     -1.     -3.      0.      1.      3.
+     -6.      2.     -4.     -7.     -8.     -5.     -7.     -7.     -3.     -5.     -2.     -3.     -4.      0.     -6.     -2.     -5.     17.
+     -3.     -4.     -2.     -4.      0.     -4.     -4.     -5.      0.     -1.     -1.     -4.     -2.      7.     -5.     -3.     -3.      0.     10.
+      0.     -2.     -2.     -2.     -2.     -2.     -2.     -1.     -2.      4.      2.     -2.      2.     -1.     -1.     -1.      0.     -6.     -2.      4.
+//

data/test/data/aaindex/PRAM900102

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+H PRAM900102
+D Relative frequency in alpha-helix (Prabhakaran, 1990)
+R LIT:1614053b PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in 
+  signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original reference of these three data: 
+  Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman, 
+  W.H., ed.), San Francisco P.235 (1983)
+C LEVM780101    1.000  LEVM780104    0.964  PALJ810101    0.943
+  KANM800101    0.942  ISOY800101    0.929  MAXF760101    0.924
+  ROBB760101    0.916  GEIM800101    0.912  GEIM800104    0.907
+  RACS820108    0.904  PALJ810102    0.902  PALJ810109    0.898
+  NAGK730101    0.894  CRAJ730101    0.887  CHOP780201    0.873
+  TANS770101    0.854  KANM800103    0.850  QIAN880107    0.829
+  QIAN880106    0.827  BURA740101    0.805  NAGK730103   -0.809
+I    A/L     R/K     N/M     D/F     C/P     Q/S     E/T     G/W     H/Y     I/V
+    1.29    0.96    0.90    1.04    1.11    1.27    1.44    0.56    1.22    0.97
+    1.30    1.23    1.47    1.07    0.52    0.82    0.82    0.99    0.72    0.91
+//

data/test/data/bl2seq/cd8a_cd8b_blastp.bl2seq

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+Query= CD8A_HUMAN P01732 T-cell surface glycoprotein CD8 alpha chain
+precursor (T-lymphocyte differentiation antigen T8/Leu-2).
+         (235 letters)
+
+>CD8B_HUMAN P10966 T-cell surface glycoprotein CD8 beta chain
+           precursor (Antigen CD8B).
+          Length = 210
+
+ Score = 29.6 bits (65), Expect = 5e-05
+ Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 3/90 (3%)
+
+Query: 39  VELKCQVLLSNPTSGCSWLFQ---PRGAAASPTFLLYLSQNKPKAAEGLDTQRFSGKRLG 95
+           V L C+  +S       WL Q   P   +      L+ S       E ++ ++ +  R  
+Sbjct: 37  VMLSCEAKISLSNMRIYWLRQRQAPSSDSHHEFLALWDSAKGTIHGEEVEQEKIAVFRDA 96
+
+Query: 96  DTFVLTLSDFRRENEGYYFCSALSNSIMYF 125
+             F+L L+  + E+ G YFC  + +  + F
+Sbjct: 97  SRFILNLTSVKPEDSGIYFCMIVGSPELTF 126
+
+
+Lambda     K      H
+   0.323    0.137    0.436 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 102
+Number of Sequences: 0
+Number of extensions: 5
+Number of successful extensions: 3
+Number of sequences better than 10.0: 1
+Number of HSP's better than 10.0 without gapping: 1
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 0
+Number of HSP's gapped (non-prelim): 1
+length of query: 235
+length of database: 210
+effective HSP length: 22
+effective length of query: 213
+effective length of database: 188
+effective search space:    40044
+effective search space used:    40044
+T: 11
+A: 40
+X1: 16 ( 7.5 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 20 (12.2 bits)
+S2: 20 (12.3 bits)

data/test/data/bl2seq/cd8a_p53_e-5blastp.bl2seq

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+Query= CD8A_HUMAN P01732 T-cell surface glycoprotein CD8 alpha chain
+precursor (T-lymphocyte differentiation antigen T8/Leu-2).
+         (235 letters)
+
+Lambda     K      H
+   0.323    0.137    0.436 
+
+Gapped
+Lambda     K      H
+   0.267   0.0410    0.140 
+
+
+Matrix: BLOSUM62
+Gap Penalties: Existence: 11, Extension: 1
+Number of Hits to DB: 175
+Number of Sequences: 0
+Number of extensions: 8
+Number of successful extensions: 0
+Number of sequences better than 1.0e-05: 0
+Number of HSP's better than  0.0 without gapping: 0
+Number of HSP's successfully gapped in prelim test: 0
+Number of HSP's that attempted gapping in prelim test: 0
+Number of HSP's gapped (non-prelim): 0
+length of query: 235
+length of database: 393
+effective HSP length: 27
+effective length of query: 208
+effective length of database: 366
+effective search space:    76128
+effective search space used:    76128
+T: 11
+A: 40
+X1: 16 ( 7.5 bits)
+X2: 38 (14.6 bits)
+X3: 64 (24.7 bits)
+S1: 41 (22.0 bits)
+S2: 74 (33.1 bits)