generating exon alignments

[Navin Rustagi]

Hi, 

 

I have to generate alignements in the exonic regions between multiple species. Are the alignments generated in phase for translation ? 

Regards, 

Navin 

[Pauline Fujita]

Hello Navin,

We're not sure how you are generating your alignments so it's
difficult to say. Generally speaking we don't think you would consider
them in phase. Hopefully my colleague's reply to your other question
has gotten you the information you need. If you still have further
questions please feel free to contact the mailing list again at
gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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[Navin Rustagi]

Hi pauline,

Thanks for your response.

Well I can share with you my workflow, if that would help you decide if the alignments which i have are indeed phase preserved. For my purposes it is suffiicient that at least the human sequences are not our of phase. If there is a way to ensure that, then it is great.

Regards,

Navin

[Brooke Rhead]

Hi Navin,

If you are using the Table Browser to and the "CDS FASTA" output format,
then the CDS alignments from the UCSC Genes track (table: knownGene) are
in phase. If you are using RefSeq Genes (table: refGene), a few of the
refGene exons might not be in phase after the first exon since the mRNA
may have bases in it that aren't in the reference sequence, but the huge
majority will be in phase.

--
Brooke Rhead
UCSC Genome Bioinformatics Group