Bioinformatics

SimpleX theme shadow.png problem fix

By Haktan Suren, PhD

1 Comment

Oct 3rd, 2012

If you are using simplex theme for your wordpress, you are probably having shadow.png not found (404) error while loading the webpage. I know this is v...

Google Fonts: Make your website even prettier!

By Haktan Suren, PhD

0 Comments

Oct 3rd, 2012

I would like to share something that I have recently discovered, Google Fonts. It is awesome!. It will definitely change the way your website looks sig...

VI: format your custom database by replace function

By Haktan Suren, PhD

0 Comments

Oct 3rd, 2012

Couple days ago, I used nucleotide seqs from JGI website and had to create my own blast database. Before I do that, I had to get rid of some of the ext...

Building a BLAST database with local sequences : makeblastdb

By Haktan Suren, PhD

0 Comments

Oct 3rd, 2012

Building a BLAST database with local sequences has never been this easy. Follow the instructions below and create your own searchable BLAST db in secon...

Execute a program runs background via SSH

By Haktan Suren, PhD

0 Comments

Oct 3rd, 2012

This is extremely helpful to automate running some program through bash Usage: Example: Output: Enjoy!...

BLAST: blastn/tblastx/blastp/tblastn/blastx

By Haktan Suren, PhD

4 Comments

Oct 3rd, 2012

if you need only one best hit for each query, use -num_alignments and -num_descriptions flag as fallows. Usage: Example: Output: Enjoy!...

BLAST: fastacmd

By Haktan Suren, PhD

4 Comments

Oct 3rd, 2012

I ll list two useful commands of this function. 1-) Get a brief summary about the BLAST database Usage: Example: Output: 2-) Get sequence(s) of a given...