454 Sequences analysis!!

[alessandra85]

Hi everybody!!!

I am trying to analyze some amplicons sequences from 454, but I need some advice. I need to find SNP in my sequences, synonym substitutions and non synonym and haplotypes; but I don’t know what kind of programs can I use? Mainly because of the .sff file format from my sequences.

I hope someone could help me

Thanks in advance

Alessandra.

[maubp]

If it is the SFF format that is worrying you, you can convert SFF into FASTQ or FASTA+QUAL which are more widely supported. I can suggest three tools for that,

Roche's own "off instrument applications" (Linux only)

sff_extract - http://bioinf.comav.upv.es/sff_extract/index.html

Biopython's SeqIO module - http://biopython.org (cross platform)

[kmcarr]

You could use the Roche/454 Amplicon Variant Analyzer software. The software is designed for processing and analyzing ultra-deep amplicon sequence data from the GS FLX system. It will read the SFF file directly and can be used via either a GUI or command line.

Roche/454 software can be obtained by request through their web site:

http://454.com/contact-us/software-request.asp