Blast Output

sequenceserver
#1

can i get blast output in différent format using sequenceserver?
like tabular form etc.

#2

Sushim Gupta wrote:

can i get blast output in différent format using sequenceserver?
like tabular form etc.

Not yet.

#3

Dear Anurag,

I have one more query. When we blast a longer sequence, we get nth number of hits for the same region with a slight difference in bit score and E-value as 0, hence, my question is that is it possible to get a specific hit for one sequence and rest other being omitted.

Thanks n Regards,
Sushim

#4

Hi Sushim,

you can restrict blast to return only hits to a single database sequence. For this, specify in the “advanced parameters”:
-max_target_seqs 1 or -num_alignments 1

From a single database sequence, blast will however return all the hits that it finds. The other way of limiting output is to

Another way of limiting your results (which also works within a single database sequence) is to increase the evalue cutoff stringency. E.g. put -evalue 1.0e-100

Hope this helps

cheers,
yannick

#5

Hi Yannick,

Thank you very much for the reply.

I would like to clarify one more thing.

Suppose a 50 kb fragment containing gene sequences for 12 genes.

If this fragment was used for the blast against my database and i keep -max_target_seqs 1 or -num_alignments 1 as one of parameter.

i will get only one hit.

If i am using the default parameter for blast, I will get the hits for the entire gene but for each gene I will get multiple hits for the same region of the query, If the database containing almost similar gene (95-99% similar). Is there any way to omit all hits from same query region and keep the best one?

Regards

Sushim