Programs for cross-species ESTs to genomic sequences alignment

[Kaidy]

Hello,

I need to align a set of EST sequences from one species to the genomic sequences from a related species. I heard that there are several programs can do this, e.g. SIM4db, C(X)AT and Pairagon etc. I wonder anyone has any experience on using these software and which one would you recommend? Thanks in advance!

[JackieBadger]

Tophat, Newbler, and BLAT are designed for this and are commonly used

[Kaidy]

Tophat, Newbler, and BLAT are designed for this and are commonly used

Hi Jackie,

Thanks a lot for the quick response. But I heard that BLAT is designed for within-species alignment, i.e. it requires high sequence similarity. In my case, the sequences from two species could be quite divergent. I am not very sure whether it would be very suitable.

[SES]

Hi Jackie,

Thanks a lot for the quick response. But I heard that BLAT is designed for within-species alignment, i.e. it requires high sequence similarity. In my case, the sequences from two species could be quite divergent. I am not very sure whether it would be very suitable.

That is correct, I think BLAT expects the query and target to be nearly identical. I would use the est2genome model from exonerate. It (exonerate) is very flexible in terms of the output formats. There is also a program called 'est2genome' that is a part of EMBOSS.

[JackieBadger]

hmmm...BLAT can be used between species as there is a mismatch switch. But indeed this depends how different the genomes are.
My main problem with BLAT is that it can be a pain

[SES]

hmmm...BLAT can be used between species as there is a mismatch switch. But indeed this depends how different the genomes are.
My main problem with BLAT is that it can be a pain

I stand corrected. A quick search shows that the original paper does describe cross-species alignments. Though, I didn't check in detail (just glanced the abstract) it is worth considering what level of divergence is expected. I haven't used BLAT very much myself (I, too remember it being difficult), but I have used exonerate quite a bit for cross-species EST alignment.

[GenoMax]

@kaidy: Can you clarify if these are NGS sequences (short) or have they been assembled into longer contigs? If the species are very divergent then something like lastz would be worth a try.