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'''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | '''cufflinks''' [http://cufflinks.cbcb.umd.edu/] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples | ||
'''dbget''' | '''dbget''' DBGET is an integrated database retrieval system for major biological databases | ||
'''denovo2''' | '''denovo2''' |
2012年6月1日 (金) 01:51時点における版
- インストール済みソフトウェア(分子生物学)
abyss [1] Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler
allpaths-lg [2] The new short read genome assembler
blast Sequence Similarity Search blast+
blat [3] BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more
bowtie [4] Bowtie is an ultrafast, memory-efficient short read aligner
bwa [5] Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence
CAP3 Multiple Sequence Alignment
clustalw Multiple Sequence Alignment clustalw2
consed Assembly Editor
cufflinks [6] Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples
dbget DBGET is an integrated database retrieval system for major biological databases
denovo2
EMBOSS [7] EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology
fasta Sequence Similarity Search
Gblocks [8] eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences genemark [9] A family of gene prediction programs
genscan [10] Gene prediction
glimmer [11] Glimmer is a system for finding genes in microbial DNA
hmmer [12] Biosequence analysis using profile HMM
IGV lastz mafft meme mrbayes muscle njplot paup Phred+Phrap phylip phyml raxml readseq samtools soap sparsehash-1.11 stacks stacks-0.996 t_coffee tgicl_linux tophat tree-puzzle trinityrnaseq velvet
- インストール済みソフトウェア(その他)
Gene Spring (端末室 Windowsマシン上 所内のみ利用可) MATLAB(同上) MATLAB Distributed Computing Server Pipeline Pilot
- 他一般ソフトウェア、プログラム言語
csh tcsh zsh bash perl ruby python gcc gcc ver.4 icc