Difference between revisions of "Priority List of Topics"
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[http://dl.dropbox.com/u/4936834/PWM_scan.zip PWM Scan] - a perl script that scans a genome or long DNA sequence for motifs that fit into a specific position weight matrix's parameters. Includes a quicker scan and a longer scan that uses every possible window. | [http://dl.dropbox.com/u/4936834/PWM_scan.zip PWM Scan] - a perl script that scans a genome or long DNA sequence for motifs that fit into a specific position weight matrix's parameters. Includes a quicker scan and a longer scan that uses every possible window. | ||
| − | [http://dl.dropbox.com/u/4936834/blastparse.py Blast Parse] - python script that will parse local blast results. Input should be the tab delimiter format as follows: QueryName Subject QueryEnd QueryStart SubjectEnd. Output can sort by any one of these elements. The default setting is to sort by Subject (in our case contigs or scaffolds). | + | [http://dl.dropbox.com/u/4936834/blastparse.py Blast Parse] - python script that will parse local blast results. Input should be the tab delimiter format as follows: QueryName Subject QueryEnd QueryStart SubjectEnd. Output can sort by any one of these elements. The default setting is to sort by Subject (in our case contigs or scaffolds). Note: to run, edit input file name to match your input file. Then type "python /pathto/blastparse.py" from terminal |
==Lauren== | ==Lauren== | ||
Revision as of 19:23, 3 February 2011
Contents
perl scripts for genome analysis
PWM Scan - a perl script that scans a genome or long DNA sequence for motifs that fit into a specific position weight matrix's parameters. Includes a quicker scan and a longer scan that uses every possible window.
Blast Parse - python script that will parse local blast results. Input should be the tab delimiter format as follows: QueryName Subject QueryEnd QueryStart SubjectEnd. Output can sort by any one of these elements. The default setting is to sort by Subject (in our case contigs or scaffolds). Note: to run, edit input file name to match your input file. Then type "python /pathto/blastparse.py" from terminal
Lauren
Glucose Metabolism
- Acid Invertase
Dylan
Myb Transcription Factors
Laura
rRNA Genes
Lexi
Puneet
Leland
Mitochondrial/Chloroplast Separation
Will
Jared
Methytransferases and RNAi Pathways
Additional Possible Topics
Lignins
Pectins
Tanins
