align transcripts to genome

Question

[Kurban]

i have a transcriptome dataset of an insect, and it's must longest transcript is 24081b, the shortest one is 101b, but its not a model species. so i want to align the dataset with the genome of Tribolium castaneum, because they belong to the same family.i am hoping by aligning my specimen' transcriptome with the genome of Tribolium castaneum to find out how many transcripts could be aligned and what r those genes function in Tribolium castaneum ?
so, by using what kind of tool could i get what i want?
looking forward tips

sincerely.

[Sean Davis]

By "transcriptome", do you mean NGS data (short reads) or do you mean FASTA sequences of your transcriptome?

[Kurban]

Maybe I was not clear before, sorry. I meant FASTA sequences of transcriptome, not NGS data.

[Sean Davis]

Thanks for the clarification. In that case, I would probably not recommend an aligner that was written for short reads (such as STAR or TopHat). If someone has evidence that these aligners do as well as more general-purpose aligners like blat and gmap, I'd love to hear it (because I don't have any data either way).

[Kurban]

i got what u meant. recently I have read a paper"STAR: ultrafast universal RNA-seq aligner", and it said STAR can align a transcript to a genome when it's length reached to around 6k, but after u recommended BLAT, I found a paper "Using BLAT to Find Sequence Similarity in Closely Related Genomes", by reading it I guess that might be the tool. thank you.

Answer 1

[Vivek]

Blat has worked like a charm on some of these projects for me.

[Kurban]

thanks . so BLAT could align a transcriptome dataset to genome at a time right? and i was told STAR also could do that, so i don't know which one is better choice. could u give me some advice on that too?

[Vivek]

I've never tried STAR but one of the main features of STAR is the alignment speed but I think you could achieve something similar with Blat by just splitting your query and submitting parallel jobs on a computing cluster.

Answer 2

[Dan D]

I would use Tophat for starters. The manual doesn't specify a top end for read length, which makes sense because Tophat chops up each read into segments and tries to map those segments early in the process.

Answer 3

[Sean Davis]

You might consider gmap, similar to blat, but much faster.

http://research-pub.gene.com/gmap/