Fasta manipulation tools???

[mbk0asis]

Hello, everyone.
I have a peak data that I can see on UCSC genome browser.
I downloaded the sequences of all the peaks in fasta format and tried to align with ClustalX/W.
but failed due to the duplicated headers (of seq ID) of the sequences.

Can anyone tell me how to change or remove the headers for multiple alignment?
Is there any software for that?

[twaddlac]

I don't know of any programs that solve that problem specifically, but you could always write some script to append an arbitrary identifier to the end of each sequence.

[gringer]

Can anyone tell me how to change or remove the headers for multiple alignment?
Is there any software for that?

For FASTA manipulation, my first port of call is FASTX-Toolkit, and then EMBOSS. A quick glance through the FASTX-Toolkit reveals a program called fastx_renamer. Here's something that should change sequence headers to a simple counter:

fastx_renamer -n COUNT -i input.fasta -o output.fasta

[mbk0asis]

Thank you very much!!!
I will try now.

[JackieBadger]

http://main.g2.bx.psu.edu/

super easy fasta manipulation. video tutorials are also very good

It employs the above programs via a GUI

[mbk0asis]

Hi, all... again.
I failed to install FastX-Toolkit on my computer (LinuxMint11 64bit - Ubuntu based).
I am trying to find what went wrong.
Meanwhile, what is the name of EMBOSS tool that can manipulate fasta files?

[gringer]

I failed to install FastX-Toolkit on my computer (LinuxMint11 64bit - Ubuntu based).

fastx-toolkit is in Debian, so it should also be in Ubuntu and Mint:

aptitude install fastx-toolkit

[mbk0asis]

# sudo aptitude install fastx-toolkit

No candidate version found for fastx-toolkit
No candidate version found for fastx-toolkit
No packages will be installed, upgraded, or removed.
0 packages upgraded, 0 newly installed, 0 to remove and 18 not upgraded.
Need to get 0 B of archives. After unpacking 0 B will be used.

???

[gringer]

It's in the oneiric and precise universe repositories from Ubuntu. Add one of those to your package repostiories list:

http://packages.ubuntu.com/search?keywords=fastx-toolkit&searchon=names&suite=all&section=all

[dvanic]

To completely remove the headers just use awk:

cat fasta.filename | awk '0 == NR % 2' > sequences_only

But the FASTX-toolkit is in general quite a useful utility to have, so perhaps have a look at the instructions here:
http://hannonlab.cshl.edu/fastx_tool...all_ubuntu.txt and here:
http://hannonlab.cshl.edu/fastx_toolkit/download.html

Hope this helps!

[gringer]

To completely remove the headers just use awk

Here's a perl one-liner which will replace fasta headers with the current input line number:

perl -pe 's/^>.*$/">$."/e' input.fasta > output.fasta

Same thing with awk:

awk '{if(/^>/){print ">"FNR} else{print $0}}' input.fasta > output.fasta

[mbk0asis]

Finally, it worked, GRINGER.

I really really appreciate your help.