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RepeatMasker安装与使用  

2013-11-19 11:29:21|  分类: 生信分析软件 |  标签: |举报 |字号 订阅

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http://www.repeatmasker.org/RMDownload.html
http://fhqdddddd.blog.163.com/blog/static/1869915420139160262497/

1.       序列搜索引擎

HMMER, Cross_Match, RMBlast and WUBlast/ABBlast are supported
本人安装的RMBlast http://www.repeatmasker.org/RMBlast.html

2.       TRF(Tandem Repeat Finder)搜寻串联重复序列

http://tandem.bu.edu/trf/trf.download.html

3.       RepeatMasker程序

http://www.repeatmasker.org/RMDownload.html 2/21/2013: RepeatMasker-open-4-0-1.tar.gz

tar xvzf RepeatMasker-open-4-0-1.tar.gz #解压

数据库http://www.girinst.org/server/RepBase/index.php

repeatmaskerlibraries-20130422.tar.gz (26.76 MB) 5/1/2013最新版,这个要注册申请。

cp repeatmaskerlibraries-20130422.tar.gz RepeatMasker/ #复制库到程序目录

tar xvzf repeatmaskerlibraries-20120418.tar.gz #解压并覆盖原库

perl ./configure #主要是输入,PERL,RMBlast,TRF,HMMER安装目录

4. 以拟南芥为例进行标记重复序列

 RepeatMasker -pa 8 -species arabidopsis TAIR10_chr_all.fas

具体参数:

RepeatMasker -h
RepeatMasker version open-4.0.3
Option h is ambiguous (help, html)
NAME
    RepeatMasker - Mask repetitive DNA

SYNOPSIS
      RepeatMasker [-options] <seqfiles(s) in fasta format>

DESCRIPTION
    The options are:

    -h(elp)
        Detailed help

    Default settings are for masking all type of repeats in a primate
    sequence.

    -e(ngine) [crossmatch|wublast|abblast|ncbi|hmmer|decypher]
        Use an alternate search engine to the default.

    -pa(rallel) [number]
        The number of processors to use in parallel (only works for batch
        files or sequences over 50 kb)

    -s  Slow search; 0-5% more sensitive, 2-3 times slower than default

    -q  Quick search; 5-10% less sensitive, 2-5 times faster than default

    -qq Rush job; about 10% less sensitive, 4->10 times faster than default
        (quick searches are fine under most circumstances) repeat options

    -nolow /-low
        Does not mask low_complexity DNA or simple repeats

    -noint /-int
        Only masks low complex/simple repeats (no interspersed repeats)

    -norna
        Does not mask small RNA (pseudo) genes

    -alu
        Only masks Alus (and 7SLRNA, SVA and LTR5)(only for primate DNA)

    -div [number]
        Masks only those repeats < x percent diverged from consensus seq

    -lib [filename]
        Allows use of a custom library (e.g. from another species)

    -cutoff [number]
        Sets cutoff score for masking repeats when using -lib (default 225)

    -species <query species>
        Specify the species or clade of the input sequence. The species name
        must be a valid NCBI Taxonomy Database species name and be contained
        in the RepeatMasker repeat database. Some examples are:

          -species human
          -species mouse
          -species rattus
          -species "ciona savignyi"
          -species arabidopsis

        Other commonly used species:

        mammal, carnivore, rodentia, rat, cow, pig, cat, dog, chicken, fugu,
        danio, "ciona intestinalis" drosophila, anopheles, elegans,
        diatoaea, artiodactyl, arabidopsis, rice, wheat, and maize

    Contamination options

    -is_only
        Only clips E coli insertion elements out of fasta and .qual files

    -is_clip
        Clips IS elements before analysis (default: IS only reported)

    -no_is
        Skips bacterial insertion element check

    Running options

    -gc [number]
        Use matrices calculated for 'number' percentage background GC level

    -gccalc
        RepeatMasker calculates the GC content even for batch files/small
        seqs

    -frag [number]
        Maximum sequence length masked without fragmenting (default 60000,
        300000 for DeCypher)

    -nocut
        Skips the steps in which repeats are excised

    -noisy
        Prints search engine progress report to screen (defaults to .stderr
        file)

    -nopost
        Do not postprocess the results of the run ( i.e. call ProcessRepeats
        ). NOTE: This options should only be used when ProcessRepeats will
        be run manually on the results.

    output options

    -dir [directory name]
        Writes output to this directory (default is query file directory,
        "-dir ." will write to current directory).

    -a(lignments)
        Writes alignments in .align output file

    -inv
        Alignments are presented in the orientation of the repeat (with
        option -a)

    -lcambig
        Outputs ambiguous DNA transposon fragments using a lower case name.
        All other repeats are listed in upper case. Ambiguous fragments
        match multiple repeat elements and can only be called based on
        flanking repeat information.

    -small
        Returns complete .masked sequence in lower case

    -xsmall
        Returns repetitive regions in lowercase (rest capitals) rather than
        masked

    -x  Returns repetitive regions masked with Xs rather than Ns

    -poly
        Reports simple repeats that may be polymorphic (in file.poly)

    -source
        Includes for each annotation the HSP "evidence". Currently this
        option is only available with the "-html" output format listed
        below.

    -html
        Creates an additional output file in xhtml format.

    -ace
        Creates an additional output file in ACeDB format

    -gff
        Creates an additional Gene Feature Finding format output

    -u  Creates an additional annotation file not processed by
        ProcessRepeats

    -xm Creates an additional output file in cross_match format (for
        parsing)

    -fixed
        Creates an (old style) annotation file with fixed width columns

    -no_id
        Leaves out final column with unique ID for each element (was
        default)

    -e(xcln)
        Calculates repeat densities (in .tbl) excluding runs of >=20 N/Xs in
        the query

SEE ALSO
        Crossmatch, ProcessRepeats

COPYRIGHT
    Copyright 2007-2012 Arian Smit, Institute for Systems Biology

AUTHORS
    Arian Smit <asmit@systemsbiology.org>

    Robert Hubley <rhubley@systemsbiology.org>
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