[Genome] Blat search - chrM vs. chr17

[Brooke Rhead]

Hello Soumen,

Are you using our web-based BLAT at 
http://genome.ucsc.edu/cgi-bin/hgBlat , or are you running your own 
command-line BLAT server?

What organism and assembly are you BLATing against?  For instance, are 
you using the human, March 2006 assembly?

Are you saying that you previously got a BLAT hit on chromosome M only, 
but now the same search is returning a hit on chromosome 17 only?

--
Brooke Rhead
UCSC Genome Bioinformatics Group


From: Soumen Chakraborty <soumen_ils at yahoo.co.in>
Date: Tue, 15 Apr 2008 09:51:05 +0530 (IST)
To: genome at soe.ucsc.edu
To: genome at soe.ucsc.edu


Hi,

I am using your Blat search. However I am getting chromosome M (which I 
came to know later on is mitochondria chromosome). Now same match is 
there with chromosome 17 e.g.,

*GATCTAAAAC ACTCTTTACG CCGGCTTCTA TTGACTTGGG TTAATCGTGT  *

*GACCGCGGTG GCTGGCACGA AATTGACCAA CCCTGGGGTT AGTATAGCTT  *

*AGTTAAACTT TCGTTTATTG CTAAAGGTTA ATCACTGCTG TTTCCCGTGG  *

*GGGTGTGGCT AGGCTAaGCG TTTTGAGCTG CATTGCTGCG TGCTTGATGC  *

*TTgTCCCTTT TGATC*


Now which one is ok.

Soumen Chakraborty, Ph.D Dept. of Gene Function and Regulation
Institute of Life Sciences
Nalco Square, Chandrashekharpur
Bhubaneswar-751023, Orissa
India
Phone No: 011-91-674-2302420 (Direct)
           011-91-674-2301460 (extn-207)
Fax No:   011-91-674-2300728
www.ils.res.in <http://www.ils.res.in/>



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