I have blasted my query sequence against the subject sequence, which is Homo sapiens integrin subunit alpha 2b (ITGA2B), RefSeqGene (LRG_479) on chromosome 17.
Which showed 100 % coverage. The problem is whenever i tried to find the subject sequence in that gene, I could not!
I did that by using navigation tool in MS word.
I reverse complemented, reversed, complemented the query sequence. Still it did not show me the match. What is the solution??
Try using the genome browser gateway
http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=480650415_BqaXbSydjy6bYAEZhV7e8h2phioI
Here is ITGA2B aligned with human chr17:
http://genome.ucsc.edu/cgi-bin/hgc?hgsid=480650415_BqaXbSydjy6bYAEZhV7e8h2phioI&g=htcCdnaAliInWindow&i=NM_000419&c=chr17&l=44367824&r=44393956&o=44372180&aliTable=refSeqAli&table=refGene
Hi,
What reference are you blasting against: the human genome reference assembly, or RefSeq cDNAs? What tool are using? What sequence are you checking your query sequence against afterward (ITGA2B's cDNA or genomic sequence)?
It's possible that the subject sequence you submitted spans exon-exon junctions. If that's the case, you will not find the query sequence in its entirety if you're then looking at the genomic sequence of the gene (including introns) because it only parts of it align contiguously. Or you could have the opposite situation, where your query sequence aligns at least partially to an intronic region, but then you're checking the sequence against the cDNA.
See the attached link for an example of BLAST'ing the first three exons of ITGA2B to the human genome, using "megablast" (which is optimized for highly similar sequences). The first link is the BLAST query page with the necessary info, and the second link is the results (but will only be available for a few days). You'll notice that there is only one hit, and it's split into three matches, and you see the alignment for each of the three ranges.
Hopefully this helps, but you are free to ask more questions if you're still stuck.
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastSearch&VIEW_SEARCH=on&UNIQ_SEARCH_NAME=A_SearchOptions_1adpjE_2PYT_dsJkJKsqUQZ_23turP_1rdoxD
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=E1MUBSJJ01R
hello Kim,
Use multiple sequence alignment and find it out
http://www.ebi.ac.uk/Tools/msa/muscle/
paste both of your sequence in fasta format and submit
>seq1
>seq2
in the box and submit
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