chained blastz alignments

Question

[Pei]

Hi:

Is there any one can tell me how to convert the chained blastz alignments format into aligned nucleotides sequence?

(I have already had a similar post in this forum but no replies yet, here I just try to make the problem more clear)

Thanks in advance!

Best

Answer 1

[Pei]

Below is a kind message from UCSC staff:

You should take a look at the Axt and MAF formats (http://genome.ucsc.edu/goldenPath/help/axt.html and http://genome.ucsc.edu/FAQ/FAQformat.html#format5) to see if those meet your needs. If so, we have some conversion utilities, chainToAxt and axtToMaf, that will convert your chain files. These utilities can be downloaded from http://hgdownload.cse.ucsc.edu/admin/exe/.

HTH!