What Is Represented By Tname In Psl Format

Question

[Chami]

I am writing a Java program to fetch a short DNA sequence from a file and run a BLAT query on that.

The results I get are in PSL format.

The aim of the exercise is to see where the sequence maps to. Not just the chromosome, strand, start and end coordinates, but when available mRNA/Exon/Intron etc.

when I run it for a sequence that map to 'Homo sapiens small nucleolar RNA host gene 11 (non-protein coding) (SNHG11), non-coding RNA.'

the tName field gives a value : 63025520

Can anyone please explain what this number(tName) means and any easy way to map it to a description of the region.

Thanking in advance,

Chami

Answer 1

[Casey Bergman]

tName = target sequence name, see: http://genome.ucsc.edu/FAQ/FAQformat.html#format2

[Jeremy Leipzig]

you're probably off by a field. show us an entire line in your psl.

[Chami]

Thanks for your answer.

I did go through this resource. But my question was in the BLAT results on my query I get this 'number' 63025520 instead of something like 'Homo sapiens small nucleolar RNA host gene 11 (non-protein coding) (SNHG11), non-coding RNA.'

Can I derive at the description from that number?

Thanks

[Neilfws]

Please try to be more specific in your questions. Casey's answer is the correct one to your original question as written.