Question: trying to reproduce mirbase blastn
0
gravatar for shinken123
11 months ago by
shinken12380
México
shinken12380 wrote:

Hi

I am trying to reproduce blastn results from the mirbase webpage. Using this:

blastn -query query -db db  -max_target_seqs 100 -reward 5 -penalty -4 -num_threads 8 -word_size 4 -evalue 10 -outfmt "6 qseqid sseqid positive evalue"

and

blastn -query query -db db  -task blastn-short -max_target_seqs 100 -reward 5 -penalty -4 -num_threads 8 -word_size 4 -evalue 10 -outfmt "6 qseqid sseqid positive evalue"

However, using both commands I am getting the next errors:

Error: Gap existence and extension values 0 and 0 are not supported for substitution scores 5 and -4 
10 and 6 are supported existence and extension values


Error:Gap existence and extension values 5 and 2 are not supported for substitution scores 5 and -4 
10 and 6 are supported existence and extension values

I am using this blast version: 2.2.31+

I don't know the blast version that they use. Could some one help me reproduce mirbase blastn?

Thank you in advance,

Eric

blastn mirbase • 331 views
ADD COMMENTlink written 11 months ago by shinken12380

Try this: C: Trying to reproduce mirbase results locally with BLAST

ADD REPLYlink written 11 months ago by genomax62k

For some reason that doesn't work.

ADD REPLYlink written 10 months ago by shinken12380
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