Question: Frameshift Correction For 454 Sequence
3
gravatar for Zhenhai Zhang
8.2 years ago by
Zhenhai Zhang170
502 Wartik Lab, Penn State Univ
Zhenhai Zhang170 wrote:

I'm currently working on 454 sequencing of collection of antibodies. However, whenever there is continuous A/C/G/T (AAAAAA), a frameshift may happen by chance. As a result, the nucleotide sequence identity (to germ line) is very high but the protein sequence identify is very low.

Any idea how to correct the frameshift using python script? Or any recommendation of matured tools?

Also, please bear in your mind that the antibody sequence has very high mutation rate.

Thanks a lot!

python • 2.1k views
ADD COMMENTlink modified 8.2 years ago by Nick Loman110 • written 8.2 years ago by Zhenhai Zhang170

This in fact a much more common problem. Sequencing errors lead to frameshifts in reading frames which causes the translated sequence to not align with the target sequence. The problem is common in BlastX. The result is that you get 2 different hits (in frames) for the same target sequence. I have suggested projects to rewrite BlastX a few times (allowing 1 nucleotide gaps instead of just full amino acid gaps) since it is in fact quite irritating that a basic tool like that cannot handle real sequences. If it hasn't been done by now maybe we should just do it.

ADD REPLYlink written 8.2 years ago by Chris Evelo10.0k

This in fact a much more common problem. Sequencing errors lead to frameshifts in reading frames which causes the translated sequence to not align with the target sequence. The problem is common in BlastX. The result is that you get 2 different hits (in different frames) for the same target sequence. I have suggested projects to rewrite BlastX a few times (allowing 1 nucleotide gaps instead of just full amino acid gaps). It is in fact quite irritating that a basic tool like that cannot handle real sequences. If it hasn't been done by now maybe we should just do it.

ADD REPLYlink written 8.2 years ago by Chris Evelo10.0k
1
gravatar for Nick Loman
8.2 years ago by
Nick Loman110
Nick Loman110 wrote:

BLAST-Extend-Repraze might be useful (http://ber.sourceforge.net/)

ADD COMMENTlink written 8.2 years ago by Nick Loman110
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