[Genome] BLAT match, score, percentage - how to select best alignment

[Anton Kratz]

Hi,

I am aligning some 10.000s of sequences against the human genome with BLAT
gfServer/gfClient. One sequence = one psl outputfile. Often I get several
alignments for each sequence. I would like to know how to best interpret
(parse) the psl-output; I only want to select one single (the best)
alignment. I am unsure how to determine which alignment is most probably the
"real" position of my sequence.



   - Can I just take the alignment that has the highest number in the
   "match"-column and take this entry as the "best" alignment?



   - The order in which the alignments appear in a psl-file, has this
   something to do with the quality of the alignment?



   - Why does the UCSC BLAT-website produce a score and percentage value
   (unlike the standalone BLAT), and what is the idea behind these values? I
   tried to understand what score and percentage value mean from looking at the
   source-code in the FAQ-Entry (how to reproduce those values), but do not
   understand the actual meaning of the values.


Thanks a lot,
Anton