Bioinformatics18 blast process *blast blastall -d /share/blastdb/nr -i joungyujin_seq_040710.seq -m 8 -e 1e-10 -o joungyujin_seq_040710.seq.nr.blast -p blastx > joungyujin_seq_040710.seq.nr.blast.err & *1st_highest 1st_highest.sh joungyujin_seq_040710.seq.nr.blast > joungyujin_seq_040710.seq.nr.blast.1st.highest *add_desc add_desc.sh -i joungyujin_seq_040710.seq.nr.blast.1st.highest -d /share/blastdb/nr > joungyujin_seq_04071.. 2010. 5. 10. TIGR row data replace row data format chr01 TIGR5 gene 9450 12717 . + . ID=chr01.t00003;Name=monocopper oxidase precursor, putative, expressed replace pattern %s/ID=\(.\+\);Name=\(.\+\)/ID=\1;Name=\1;Note=\2 2008. 12. 15. R and BioConductor install R and BioConductor install How to download and install R and bioconductor 1. Downloading and unpacking R from www.r-project.org Go to www.r-project.org and download the newest R source package Newest direct link: http://mirrors.sunsite.dk/cran/src/base/R-1.8.1.tgz Lates version on sunsite: http://mirrors.sunsite.dk/cran/src/base/R-latest.tgz or in shell: wget http://mirrors.sunsite.dk/cran/src/b.. 2008. 9. 2. Spidey Parameter SPIDEY arguments: -i Input file -- genomic sequence(s) [File In] -m Input file -- mRNA sequence(s) [File In] -p Print alignment? 0=summary+alignments, 1=summary, 2=alignments, 3=summary&alignments in different files [Integer] Optional default = 0 -o Output file 1 (summary or summary+aln) [String] Optional default = stdout -a Output file 2 (alignments) [String] Optional default = spidey.aln -G In.. 2007. 12. 5. Spidey - mRNA-to-genomic alignment program Spidey -- design and overview Created by Sarah Wheelan, Spidey is written in C, and uses the NCBI Toolkit. It relies heavily on the alignment manager, which is an indexing system used to easily manage and quickly access alignments and sets of alignments. Spidey was written with two main goals in mind: find good alignments regardless of intron size; and avoid getting confused by nearby pseudogene.. 2007. 12. 5. formatdb Formatdb README ------------------ Table of Contents Introduction Command Line Options Configuration File Formatdb Notes/Troubleshooting A The -o option and identifiers B "SORTFiles failed" message C Formatting large FASTA files D Piping a database to formatdb without uncompressing E Creating custom databases. F General troubleshooting tips. G "SeqIdParse Failure" error H "FileOpen" error Append.. 2007. 12. 3. 이전 1 2 3 다음