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Committer: Package Import Robot
Author(s): Andreas Tille
Date: 2017-03-31 14:01:39 UTC
Revision ID: package-import@ubuntu.com-20170331140139-povxg86r196gejfa

Tags: upstream-3+dfsg

Import upstream version 3+dfsg

files added:

AUTHORS

COPYING

ChangeLog

Makefile.am

NEWS

README

configure.ac

data

data/CVPBR322

data/GTPA_HUMAN

data/MYSA_HUMAN

data/R76849.seq

data/blosum100.cmp

data/blosum30.cmp

data/blosum45.cmp

data/blosum50.cmp

data/blosum62.cmp

data/blosum65.cmp

data/blosum80.cmp

data/coils.prf

data/ecp.prf

data/gonnet.cmp

data/pam120.cmp

data/pam160.cmp

data/pam200.cmp

data/pam220.cmp

data/pam250.cmp

data/pam30.cmp

data/pam40.cmp

data/pam400.cmp

data/pam80.cmp

data/pfam_sh3.hmm

data/pfam_sh3.prf

data/prosite13.prf

data/score.lis

data/sh3.gpr

data/sh3.msf

data/sh3.prf

data/sh3.seq

data/standard.random

data/test.out

data/test.sh

doc/profile.txt

man/2ft.1

man/6ft.1

man/gtop.1

man/htop.1

man/pfmake.1

man/pfscale.1

man/pfscan.1

man/pfsearchV2.1

man/pfw.1

man/psa2msa.1

man/ptof.1

man/ptoh.1

src/C

src/C/Makefile.am

src/C/generic

src/C/generic/heuristic.c

src/C/generic/xali1_old.c

src/C/generic/xalip.c

src/C/include

src/C/include/profile.h

src/C/include/sequence.h

src/C/include/system.h

src/C/prg

src/C/prg/numa_threads.h

src/C/prg/pfsearch.c

src/C/prg/testHeuristic.c

src/C/prg/testHeuristicMatchDeletion.c

src/C/prg/testXali1.c

src/C/prg/testheader.c

src/C/prg/threads.h

src/C/sse2

src/C/sse2/heuristic_sse2.c

src/C/sse2/sse2_inline_fcts.h

src/C/sse2/xali1_sse2.c

src/C/sse2/xalip_sse2.c

src/C/sse2/xalit_sse2.c

src/C/sse41

src/C/sse41/heuristic_sse41.c

src/C/sse41/xali1_sse41.c

src/C/sse41/xalip_sse41.c

src/C/sse41/xalit_sse41.c

src/C/utils

src/C/utils/Normalization.c

src/C/utils/ReadSequence.c

src/C/utils/io.c

src/C/utils/output.c

src/Fortran

src/Fortran/2ft.f

src/Fortran/6ft.f

src/Fortran/CFAve.f

src/Fortran/CPAve.f

src/Fortran/Makefile.am

src/Fortran/NtoR.f

src/Fortran/RtoN.f

src/Fortran/Xblnk.f

src/Fortran/abini.f

src/Fortran/ardim.f

src/Fortran/avdat.f

src/Fortran/codat.f

src/Fortran/cvini.f

src/Fortran/dfdat.f

src/Fortran/dfnul.f

src/Fortran/djdat.f

src/Fortran/gsdat.f

src/Fortran/gtop.f

src/Fortran/hmdat.f

src/Fortran/htop.f

src/Fortran/io.c

src/Fortran/lblnk.f

src/Fortran/nodat.f

src/Fortran/pfdat.f

src/Fortran/pfind.f

src/Fortran/pfmake.f

src/Fortran/pfscale.f

src/Fortran/pfscan.f

src/Fortran/pfsearch.f

src/Fortran/pfsearchV2.f

src/Fortran/pfw.f

src/Fortran/pmali.f

src/Fortran/prali.f

src/Fortran/prsp.f

src/Fortran/prxp.f

src/Fortran/psa2msa.f

src/Fortran/psdat.f

src/Fortran/ptof.f

src/Fortran/ptoh.f

src/Fortran/pxdat.f

src/Fortran/recmd.f

src/Fortran/regpr.f

src/Fortran/remsa.f

src/Fortran/remsf.f

src/Fortran/reprf.f

src/Fortran/reseq.f

src/Fortran/rfseq.f

src/Fortran/rhmmer.f

src/Fortran/rhmmer2.f

src/Fortran/rhnul.f

src/Fortran/schmm.f

src/Fortran/sterr.f

src/Fortran/wprsm.f

src/Fortran/wrhmr.f

src/Fortran/wrprf.f

src/Fortran/wrsam.f

src/Fortran/xali1.f

src/Fortran/xalip.f

src/Fortran/xalit.f

src/Fortran/xprsm.f

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data/blosum65.cmp

# Matrix made by matblas from blosum65.iij

# * column uses minimum score

# BLOSUM Clustered Scoring Matrix in 1/2 Bit Units

# Blocks Database = /data/blocks_5.0/blocks.dat

# Cluster Percentage: >= 65

# Entropy = 0.7576, Expected = -0.5675

# mean= -1.0322 , stdev= 2.3266

A B C D E F G H I K L M N P Q R S T V W Y Z ..

4.0 -2.0 0.0 -2.0 -1.0 -2.0 0.0 -2.0 -1.0 -1.0 -2.0 -1.0 -2.0 -1.0 -1.0 -1.0 1.0 0.0 0.0 -3.0 -2.0 -1.0 A

4.0 -3.0 4.0 1.0 -3.0 -1.0 0.0 -3.0 0.0 -4.0 -3.0 3.0 -2.0 0.0 -1.0 0.0 -1.0 -3.0 -4.0 -3.0 1.0 B

9.0 -4.0 -4.0 -2.0 -3.0 -3.0 -1.0 -3.0 -1.0 -2.0 -3.0 -3.0 -3.0 -4.0 -1.0 -1.0 -1.0 -2.0 -2.0 -4.0 C

6.0 2.0 -4.0 -1.0 -1.0 -3.0 -1.0 -4.0 -3.0 1.0 -2.0 0.0 -2.0 0.0 -1.0 -3.0 -5.0 -3.0 1.0 D

5.0 -3.0 -2.0 0.0 -3.0 1.0 -3.0 -2.0 0.0 -1.0 2.0 0.0 0.0 -1.0 -3.0 -3.0 -2.0 4.0 E

6.0 -3.0 -1.0 0.0 -3.0 0.0 0.0 -3.0 -4.0 -3.0 -3.0 -2.0 -2.0 -1.0 1.0 3.0 -3.0 F

6.0 -2.0 -4.0 -2.0 -4.0 -3.0 -1.0 -2.0 -2.0 -2.0 0.0 -2.0 -3.0 -3.0 -3.0 -2.0 G

8.0 -3.0 -1.0 -3.0 -2.0 1.0 -2.0 1.0 0.0 -1.0 -2.0 -3.0 -2.0 2.0 0.0 H

4.0 -3.0 2.0 1.0 -3.0 -3.0 -3.0 -3.0 -2.0 -1.0 3.0 -2.0 -1.0 -3.0 I

5.0 -3.0 -2.0 0.0 -1.0 1.0 2.0 0.0 -1.0 -2.0 -3.0 -2.0 1.0 K

4.0 2.0 -4.0 -3.0 -2.0 -2.0 -3.0 -1.0 1.0 -2.0 -1.0 -3.0 L

6.0 -2.0 -3.0 0.0 -2.0 -2.0 -1.0 1.0 -2.0 -1.0 -2.0 M

6.0 -2.0 0.0 0.0 1.0 0.0 -3.0 -4.0 -2.0 0.0 N

8.0 -1.0 -2.0 -1.0 -1.0 -2.0 -4.0 -3.0 -1.0 P

6.0 1.0 0.0 -1.0 -2.0 -2.0 -2.0 3.0 Q

6.0 -1.0 -1.0 -3.0 -3.0 -2.0 0.0 R

4.0 1.0 -2.0 -3.0 -2.0 0.0 S

5.0 0.0 -3.0 -2.0 -1.0 T

4.0 -3.0 -1.0 -2.0 V

10.0 2.0 -3.0 W

7.0 -2.0 Y

4.0 Z

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