Wise2 Package 2.4.1 설치 - CentOS 6

Wise2 : 단백질 서열 혹은 HMM(개별 혹은 라이브러리)를 참조하여 주어진 genome sequence에서 유전자를 예측하는 프로그램

URL : http://www.ebi.ac.uk/~birney/wise2/

# yum install glib-devel-1.2.10-33.el6.x86_64    // subseqhash.h:9:18: error: glib.h: No such file or directory

# wget http://www.ebi.ac.uk/~birney/wise2/wise2.4.1.tar.gz

# tar zxvfp wise2.4.1.tar.gz

# cd wise2.4.1/src/HMMer2/

# cd HMMer2

# sed -i -e 's/getline/getlineSeq/g' sqio.c  // sqio.c:232: error: conflicting types for ‘getline’

# cd ../models/

# sed -i -e 's/isnumber/isdigit/g' phasemodel.c  // phasemodel.c:(.text+0x3157): undefined reference to `isnumber'

# cd ..

# make all

# vi /etc/profile.d/wise.sh

export WISECONFIGDIR=/usr/local/src/wise2.4.1/wisecfg/

WISE2_PATH=/usr/local/src/wise2.4.1/src/bin/ 

export PATH=$PATH:$WISE2_PATH

# chmod 755 /etc/profile.d/wise.sh

# source /etc/profile.d/wise.sh

# genewise -help

genewise ($Name: wise2-4-1 $)

genewise <protein-file> <dna-file> in fasta format

Dna sequence options

  -u               start position in dna

  -v               end position in dna

  -trev            Compare on the reverse strand

  -tfor [default]  Compare on the forward strand

  -both            Both strands

  -tabs            Report positions as absolute to truncated/reverse sequence

  -fembl            File is an EMBL file native format

Protein comparison options

  -s               start position in protein

  -t               end   position in protein

  -[g]ap    [ 12]  gap penalty

  -[e]xt    [  2]  extension penalty

  -[m]atrix [BLOSUM62.bla]  Comparison matrix

HMM options

  -hmmer           Protein file is HMMer file (version 2 compatible)

  -hname           Use this as the name of the HMM, not filename

New gene model statistics

  -splice_max_collar      [5.0]  maximum Bits value for a splice site 

  -splice_min_collar      [-5.0] minimum Bits value for a splice site 

  -splice_score_offset    [1.5]  score offset for splice sites

  -[no]splice_gtag        make just gtag splice sites (default is gtag, ie no model)

  -splice_gtag_prob       [0.001] probability for gt/ag 

  -genestats              [gene.stat]

  -splice [model/flat] [LEGACY only for -splice flat. use -splice_gtag]

Phased Protein/HMM parameters (separate from other options)

  -phase_marked    [0.95]        Probability of marked introns

  -phase_unmarked  [0.00001]     Probability of unmarked introns

  -phase_file      [filename]    Intron positions and phases

  -phase_help      prints longer help on phase file and exits

Other model options

  -[no]newgene  use new gene stats (default), no for reverting to old system

  -init   [default]  [default/global/local/wing/endbias] startend policy for the HMM/protein

  -codon  [codon.table]  Codon file

  -subs   [1e-06] Substitution error rate

  -indel  [1e-06] Insertion/deletion error rate

  -null   [syn/flat]   Random Model as synchronous or flat [default syn]

  -alln   [1.0]   Probability of matching a NNN codon

  -insert [model/flat] Use protein insert model     [default flat]

Algorithm options

  -alg    [623/623L/623S/623P/2193/2193L]  Algorithm used [default 623/623L]

  (normally use 623 for proteins, 623L for HMMs and 623P for Phased Proteins)

Output options [default -pretty -para]

  -pretty          show pretty ascii output

  -pseudo          Mark genes with frameshifts as pseudogenes

  -genes           show gene structure

  -genesf          show gene structure with supporting evidence

  -embl            show EMBL feature format with CDS key

  -diana           show EMBL feature format with misc_feature key (for diana)

  -para            show parameters

  -sum             show summary output

  -cdna            show cDNA

  -trans           show protein translation, breaking at frameshifts

  -pep             show protein translation, splicing frameshifts

  -ace             ace file gene structure

  -gff             Gene Feature Format file

  -gener           raw gene structure

  -alb             show logical AlnBlock alignment

  -pal             show raw matrix alignment

  -block  [50]     Length of main block in pretty output

  -divide [//]     divide string for multiple outputs

Genewise protein running heuristics

   -[no]gwhsp        use heuristics for proteins [FALSE currently]

   -gw_edgequery     at start/end, amount of protein area to expand [10]

   -gw_edgetarget    at start/end, amount of DNA area to expand [3000]

   -gw_splicespread  spread around splice sites in codons [5]

   -gwdebug          print out debugging of heuristics on stdout

Dynamic programming matrix implementation

  -dymem       memory style [default/linear/explicit]

  -kbyte       memory amount to use [4000]

  -[no]dycache implicitly cache dy matrix usage (default yes)

  -dydebug     drop into dynamite dp matrix debugger

  -paldebug    print PackAln after debugger run if used

Standard options

  -help       help

  -version    show version and compile info

  -silent     No messages    on stderr

  -quiet      No report/info on stderr

  -erroroffstd No warning messages to stderr

  -errorlog   [file] Log warning messages to file

  -errorstyle [server/program] style of error reporting (default program)