[med-svn] r22443 - in trunk/packages/rostlab/profphd-utils/trunk/debian: . examples
Tatiana Malygina
latticetower-guest at moszumanska.debian.org
Fri Jul 8 14:05:22 UTC 2016
Author: latticetower-guest
Date: 2016-07-08 14:05:22 +0000 (Fri, 08 Jul 2016)
New Revision: 22443
Added:
trunk/packages/rostlab/profphd-utils/trunk/debian/examples/
trunk/packages/rostlab/profphd-utils/trunk/debian/examples/1ppt.hssp
trunk/packages/rostlab/profphd-utils/trunk/debian/examples/Maxhom_GCG.metric
Modified:
trunk/packages/rostlab/profphd-utils/trunk/debian/changelog
Log:
add debian/examples/ to use with testsuite
Modified: trunk/packages/rostlab/profphd-utils/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/profphd-utils/trunk/debian/changelog 2016-07-08 12:10:08 UTC (rev 22442)
+++ trunk/packages/rostlab/profphd-utils/trunk/debian/changelog 2016-07-08 14:05:22 UTC (rev 22443)
@@ -1,3 +1,10 @@
+profphd-utils (1.0.10-3) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * add debian/examples/ to use with testsuite
+
+ -- Tatiana Malygina <merlettaia at gmail.com> Fri, 08 Jul 2016 17:03:18 +0300
+
profphd-utils (1.0.10-2) unstable; urgency=medium
* Add myself to Uploaders
@@ -65,4 +72,3 @@
* Initial version
-- Laszlo Kajan <lkajan at rostlab.org> Fri, 18 Dec 2009 23:23:21 +0100
-
Added: trunk/packages/rostlab/profphd-utils/trunk/debian/examples/1ppt.hssp
===================================================================
--- trunk/packages/rostlab/profphd-utils/trunk/debian/examples/1ppt.hssp (rev 0)
+++ trunk/packages/rostlab/profphd-utils/trunk/debian/examples/1ppt.hssp 2016-07-08 14:05:22 UTC (rev 22443)
@@ -0,0 +1,135 @@
+HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991
+PDBID query
+DATE file generated on 14-Aug-12
+SEQBASE /tmp/e1IvLiOuXj/COPF-tmp20091.msf_tmp
+PARAMETER CONVERTSEQ of query
+THRESHOLD according to: ALL
+REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
+HEADER
+COMPND
+SOURCE
+AUTHOR
+SEQLENGTH 36
+NCHAIN 1 chain(s) in query data set
+NALIGN 15
+NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
+NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
+NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
+NOTATION : %IDE: percentage of residue identity of the alignment
+NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
+NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
+NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
+NOTATION : LALI: length of the alignment excluding insertions and deletions
+NOTATION : NGAP: number of insertions and deletions in the alignment
+NOTATION : LGAP: total length of all insertions and deletions
+NOTATION : LSEQ2: length of the entire sequence of the aligned protein
+NOTATION : ACCESSION: SwissProt accession number
+NOTATION : PROTEIN: one-line description of aligned protein
+NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
+NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
+NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
+NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of INSERTION IN THIS sequence
+NOTATION : dots (....) in the alignend SEQUENCE INDICATE POINTS of deletion in this sequence
+NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
+NOTATION : acid/amide form in proportion to their database frequencies
+NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
+NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
+NOTATION : NINS: number of sequences with an insertion in the test protein at this position
+NOTATION : ENTROPY: entropy measure of sequence variability at this position
+NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
+NOTATION : WEIGHT: conservation weight
+
+## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics
+ NR. ID STRID %IDE %SIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCESSION PROTEIN
+ 1 : pdb|pdb|2l60 0.54 0.00 13 36 1 24 24 0 0 24
+ 2 : E2E4L2|PYYV_ 0.46 0.00 2 36 1 35 35 0 0 35
+ 3 : P01302|PAHO_ 0.42 0.00 1 36 1 36 36 0 0 36
+ 4 : P06304|PAHO_ 0.78 0.00 1 36 1 36 36 0 0 36
+ 5 : P06305|PAHO_ 0.80 0.00 2 36 1 35 35 0 0 35
+ 6 : P09475|PPY_L 0.37 0.00 2 36 1 35 35 0 0 35
+ 7 : P15427|PAHO_ 0.42 0.00 1 36 1 36 36 0 0 36
+ 8 : P28672|NPY_C 0.46 0.00 2 36 1 35 35 0 0 35
+ 9 : P48098|PYY_L 0.40 0.00 2 36 1 35 35 0 0 35
+ 10 : Q5JQD4|PYY3_ 0.48 0.00 2 34 1 33 33 0 0 33
+ 11 : A9YZQ9|A9YZQ 0.51 0.00 2 36 1 35 35 0 0 35
+ 12 : E7F0L6|E7F0L 0.34 0.00 2 36 1 35 35 0 0 35
+ 13 : F6VPU6|F6VPU 0.51 0.00 2 36 1 35 35 0 0 35
+ 14 : G1KDC9|G1KDC 0.43 0.00 2 36 1 35 35 0 0 35
+ 15 : Q58VQ0|Q58VQ 0.37 0.00 2 36 1 35 35 0 0 35
+## ALIGNMENTS 1 - 15
+ SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
+ 1 1 G 0 0 0 4 21 AG A
+ 2 2 P 0 0 0 15 0 PPPPPPPPPPPPPP
+ 3 3 S 0 0 0 15 42 TLSLPSTPIPPSPP
+ 4 4 Q 0 0 0 15 23 KEQQKEKKKKKKKK
+ 5 5 P 0 0 0 15 0 PPPPPPPPPPPPPP
+ 6 6 T 0 0 0 15 24 EETKEHDDEEEDED
+ 7 7 Y 0 0 0 15 52 SYYYTHNNAHPSSN
+ 8 8 P 0 0 0 15 0 PPPPPPPPPPPPPP
+ 9 9 G 0 0 0 15 13 GGGGGGGGGGARGS
+ 10 10 D 0 0 0 15 27 PDNDSDEDEDGQEP
+ 11 11 D 0 0 0 15 19 DNDGNQGNDDDDDD
+ 12 12 A 0 0 0 15 12 AAAAAAAAEAVAAA
+ 13 13 P 0 0 0 16 32 STTPPSTPSSPGASS
+ 14 14 V 0 0 0 16 32 PPPVVPPAPLAPAPP
+ 15 15 E 0 0 0 16 2 EEEEEEDEEEEEEEE
+ 16 16 D 0 0 0 16 16 EEQDDDQEQEDEDEE
+ 17 17 L 0 0 0 16 12 LLMLLWLLMLVMLML
+ 18 18 I 0 0 0 16 28 NAARIAAAASAAAAS
+ 19 19 R 0 0 0 16 41 REQFQSQKRHKKRKK
+ 20 20 F 0 0 0 16 1 YYYYFYYYYYYYYYY
+ 21 21 Y 0 0 0 16 32 YMAYYQYYKYYHYFM
+ 22 22 D 0 0 0 16 35 ATADDASSAATTSSL
+ 23 23 N 0 0 0 16 34 SKENDADAASAAAAA
+ 24 24 L 0 0 0 16 8 LILLLVLLVLLLLLV
+ 25 25 Q 0 0 0 16 30 RRRQQRYRRCRRRRR
+ 26 26 Q 0 0 0 16 19 HQRQQHQHHHHHHHN
+ 27 27 Y 0 0 0 16 0 YYYYYYYYYYYYYYY
+ 28 28 L 0 0 0 16 19 LIIRLVIIILIIIII
+ 29 29 N 0 0 0 16 16 NNNLNNTNNNNNNNN
+ 30 30 V 0 0 0 16 20 LLMNVLFLLVLLLLL
+ 31 31 V 0 0 0 16 10 VVLVVIIIIVIIIVI
+ 32 32 T 0 0 0 16 9 TTTFTTTTTTTTTTT
+ 33 33 R 0 0 0 16 0 RRRRRRRRRRRRRRR
+ 34 34 H 0 0 0 16 21 QQPHPQPQQQQQQQQ
+ 35 35 R 0 0 0 15 0 RRRRRRRRR RRRRR
+ 36 36 Y 0 0 0 15 1 YYYYFYFYY YYYYY
+## SEQUENCE PROFILE AND ENTROPY
+ SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
+ 1 1 0 0 0 0 0 0 0 50 50 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0.693 50 0.93
+ 2 2 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.38
+ 3 3 0 13 7 0 0 0 0 0 0 40 27 13 0 0 0 0 0 0 0 0 15 0 0 1.437 53 0.56
+ 4 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 20 13 0 0 15 0 0 0.861 32 0.88
+ 5 5 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.38
+ 6 6 0 0 0 0 0 0 0 0 0 0 0 13 0 7 0 7 0 47 0 27 15 0 0 1.338 49 0.80
+ 7 7 0 0 0 0 0 0 27 0 7 7 20 7 0 13 0 0 0 0 20 0 15 0 0 1.807 67 0.41
+ 8 8 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.38
+ 9 9 0 0 0 0 0 0 0 80 7 0 7 0 0 0 7 0 0 0 0 0 15 0 0 0.720 27 1.09
+ 10 10 0 0 0 0 0 0 0 7 0 13 7 0 0 0 0 0 7 20 7 40 15 0 0 1.679 62 0.80
+ 11 11 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 7 0 20 60 15 0 0 1.078 40 0.99
+ 12 12 7 0 0 0 0 0 0 0 87 0 0 0 0 0 0 0 0 7 0 0 15 0 0 0.485 18 1.14
+ 13 13 0 0 0 0 0 0 0 6 6 31 38 19 0 0 0 0 0 0 0 0 16 0 0 1.392 50 0.74
+ 14 14 19 6 0 0 0 0 0 0 19 56 0 0 0 0 0 0 0 0 0 0 16 0 0 1.125 41 0.73
+ 15 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 94 0 6 16 0 0 0.234 8 1.33
+ 16 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 44 0 38 16 0 0 1.043 38 1.05
+ 17 17 6 63 0 25 0 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.987 36 1.18
+ 18 18 0 0 13 0 0 0 0 0 63 0 13 0 0 0 6 0 0 0 6 0 16 0 0 1.160 42 0.70
+ 19 19 0 0 0 0 6 0 0 0 0 0 6 0 0 6 25 31 19 6 0 0 16 0 0 1.717 62 0.60
+ 20 20 0 0 0 0 13 0 88 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.377 14 1.36
+ 21 21 0 0 0 13 6 0 56 0 6 0 0 0 0 6 0 6 6 0 0 0 16 0 0 1.450 52 0.64
+ 22 22 0 6 0 0 0 0 0 0 31 0 25 19 0 0 0 0 0 0 0 19 16 0 0 1.511 55 0.61
+ 23 23 0 0 0 0 0 0 0 0 50 0 13 0 0 0 0 6 0 6 13 13 16 0 0 1.473 53 0.68
+ 24 24 19 75 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.703 25 1.18
+ 25 25 0 0 0 0 0 0 6 0 0 0 0 0 6 0 69 0 19 0 0 0 16 0 0 0.918 33 0.73
+ 26 26 0 0 0 0 0 0 0 0 0 0 0 0 0 56 6 0 31 0 6 0 16 0 0 1.034 37 0.95
+ 27 27 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.000 0 1.38
+ 28 28 6 25 63 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 16 0 0 0.987 36 0.96
+ 29 29 0 6 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 88 0 16 0 0 0.463 17 1.05
+ 30 30 19 63 0 6 6 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 16 0 0 1.127 41 0.94
+ 31 31 44 6 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.882 32 1.18
+ 32 32 0 0 0 0 6 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 16 0 0 0.234 8 1.19
+ 33 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 16 0 0 0.000 0 1.38
+ 34 34 0 0 0 0 0 0 0 0 0 19 0 0 0 13 0 0 69 0 0 0 16 0 0 0.831 30 0.92
+ 35 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 15 0 0 0.000 0 1.38
+ 36 36 0 0 0 0 13 0 87 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.393 15 1.36
+//
Added: trunk/packages/rostlab/profphd-utils/trunk/debian/examples/Maxhom_GCG.metric
===================================================================
--- trunk/packages/rostlab/profphd-utils/trunk/debian/examples/Maxhom_GCG.metric (rev 0)
+++ trunk/packages/rostlab/profphd-utils/trunk/debian/examples/Maxhom_GCG.metric 2016-07-08 14:05:22 UTC (rev 22443)
@@ -0,0 +1,36 @@
+#****************************************************************** MAXHOM AMINO ACID EXCHANGE MATRIX ***************************************
+# table used by the GCG-package
+# see: Gribskov and Burgess NAR 14(16) 6745-6763
+# minimal value: -1.2 ; maximal value: 1.5
+# symbols: "-X!" added
+# Dayhoff table (Schwartz, R. M. and Dayhoff, M. O. [1979] in Atlas of Protein Sequence and Structure, Dayhoff, M. O. Ed,
+# pp. 353-358, National Biomedical Research Foundation, Washington D.C.) rescaled by dividing each value by the sum of its row
+# and column, and normalizing to a mean of 0 and standard deviation of 1.0. The value for FY (Phe-Tyr) = RW =1.425.
+# Perfect matches are set to 1.5 and no matches on any row are better than perfect matches.
+#============================================================================================================================================
+STRUCTURE-STATES: 1
+I/O-STATES: 1
+#============================================================================================================================================
+AA STR I/O V L I M F W Y G A P S T C H R K Q E N D B Z
+ V 1.50 0.80 1.10 0.60 0.20 -0.80 -0.10 0.20 0.20 0.10 -0.10 0.20 0.20 -0.30 -0.30 -0.20 -0.20 -0.20 -0.30 -0.20 -0.20 -0.20
+ L 0.80 1.50 0.80 1.30 1.20 0.50 0.30 -0.50 -0.10 -0.30 -0.40 -0.10 -0.80 -0.20 -0.40 -0.30 -0.10 -0.30 -0.40 -0.50 -0.50 -0.20
+ I 1.10 0.80 1.50 0.60 0.70 -0.50 0.10 -0.30 0.00 -0.20 -0.10 0.20 0.20 -0.30 -0.30 -0.20 -0.30 -0.20 -0.30 -0.20 -0.20 -0.20
+ M 0.60 1.30 0.60 1.50 0.50 -0.30 -0.10 -0.30 0.00 -0.20 -0.30 0.00 -0.60 -0.30 0.20 0.20 0.00 -0.20 -0.30 -0.40 -0.30 -0.10
+ F 0.20 1.20 0.70 0.50 1.50 1.30 1.40 -0.60 -0.50 -0.70 -0.30 -0.30 -0.10 -0.10 -0.50 -0.70 -0.80 -0.70 -0.50 -1.00 -0.70 -0.70
+ W -0.80 0.50 -0.50 -0.30 1.30 1.50 1.10 -1.00 -0.80 -0.80 0.30 -0.60 -1.20 -0.10 1.40 0.10 -0.50 -1.10 -0.30 -1.10 -0.70 -0.80
+ Y -0.10 0.30 0.10 -0.10 1.40 1.10 1.50 -0.70 -0.30 -0.80 -0.40 -0.30 1.00 0.30 -0.60 -0.60 -0.60 -0.50 -0.10 -0.50 -0.30 -0.60
+ G 0.20 -0.50 -0.30 -0.30 -0.60 -1.00 -0.70 1.50 0.70 0.30 0.60 0.40 0.20 -0.20 -0.30 -0.10 0.20 0.50 0.40 0.70 0.60 0.30
+ A 0.20 -0.10 0.00 0.00 -0.50 -0.80 -0.30 0.70 1.50 0.50 0.40 0.40 0.30 -0.10 -0.30 0.00 0.20 0.30 0.20 0.30 0.20 0.20
+ P 0.10 -0.30 -0.20 -0.20 -0.70 -0.80 -0.80 0.30 0.50 1.50 0.40 0.30 0.10 0.20 0.30 0.10 0.30 0.10 0.00 0.10 0.10 0.20
+ S -0.10 -0.40 -0.10 -0.30 -0.30 0.30 -0.40 0.60 0.40 0.40 1.50 0.30 0.70 -0.20 0.10 0.20 -0.10 0.20 0.30 0.20 0.30 0.00
+ T 0.20 -0.10 0.20 0.00 -0.30 -0.60 -0.30 0.40 0.40 0.30 0.30 1.50 0.20 -0.10 -0.10 0.20 -0.10 0.20 0.20 0.20 0.20 0.10
+ C 0.20 -0.80 0.20 -0.60 -0.10 -1.20 1.00 0.20 0.30 0.10 0.70 0.20 1.50 -0.10 -0.30 -0.60 -0.60 -0.60 -0.30 -0.50 -0.40 -0.60
+ H -0.30 -0.20 -0.30 -0.30 -0.10 -0.10 0.30 -0.20 -0.10 0.20 -0.20 -0.10 -0.10 1.50 0.50 0.10 0.70 0.40 0.50 0.40 0.40 0.50
+ R -0.30 -0.40 -0.30 0.20 -0.50 1.40 -0.60 -0.30 -0.30 0.30 0.10 -0.10 -0.30 0.50 1.50 0.80 0.40 0.00 0.10 0.00 0.10 0.20
+ K -0.20 -0.30 -0.20 0.20 -0.70 0.10 -0.60 -0.10 0.00 0.10 0.20 0.20 -0.60 0.10 0.80 1.50 0.40 0.30 0.40 0.30 0.40 0.40
+ Q -0.20 -0.10 -0.30 0.00 -0.80 -0.50 -0.60 0.20 0.20 0.30 -0.10 -0.10 -0.60 0.70 0.40 0.40 1.50 0.70 0.40 0.70 0.50 1.10
+ E -0.20 -0.30 -0.20 -0.20 -0.70 -1.10 -0.50 0.50 0.30 0.10 0.20 0.20 -0.60 0.40 0.00 0.30 0.70 1.50 0.50 1.00 0.70 1.10
+ N -0.30 -0.40 -0.30 -0.30 -0.50 -0.30 -0.10 0.40 0.20 0.00 0.30 0.20 -0.30 0.50 0.10 0.40 0.40 0.50 1.50 0.70 1.10 0.40
+ D -0.20 -0.50 -0.20 -0.40 -1.00 -1.10 -0.50 0.70 0.30 0.10 0.20 0.20 -0.50 0.40 0.00 0.30 0.70 1.00 0.70 1.50 1.10 0.90
+ B -0.20 -0.50 -0.20 -0.30 -0.70 -0.70 -0.30 0.60 0.20 0.10 0.30 0.20 -0.40 0.40 0.10 0.40 0.50 0.70 1.10 1.10 1.10 0.60
+ Z -0.20 -0.20 -0.20 -0.10 -0.70 -0.80 -0.60 0.30 0.20 0.20 0.00 0.10 -0.60 0.50 0.20 0.40 1.10 1.10 0.40 0.90 0.60 1.10
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