BOL

MetaPred2CS Web server is a meta-predictor based on Support Vector Machine (SVM) that combines 6 individual sequence based protein-protein interaction prediction methods to predict prokaryotic two-component...

Convert a SAM file to tab-delimited alignment coordinates https://gist.github.com/sjackman/7016520 #SAM #BAM #Convert #Tab

Understanding MegaBlast https://gordonlab.wustl.edu/btheta/blast/docs/megablast_readme.html #Blast #BLASTn #MegaBlast #Alignment

Whole-Genome Sequencing (WGS) PPT http://www.bx.psu.edu/~ratan/Sequence%20Analysis.pdf #PPT #WGS #Ratan

If you have > Blast 2.2.29 versions, then you need to put -max_hsps 1 parameter, and it gonna work well for you. 

I used the following command to print the blast hit. [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out...

SAM flags https://broadinstitute.github.io/picard/explain-flags.html #SAM #Flags

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

SAM and BAM handling with Perl http://search.cpan.org/~lds/Bio-SamTools/lib/Bio/DB/Sam.pm # Perl #SAM #BAM

A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and...