Question: Blastall vs Blastn
0
gravatar for sicat.paolo20
9 months ago by
sicat.paolo2030 wrote:

Good day everyone, I am currently trying a workflow that was done with blastall version 2.2.26. I wanted to update it and use the 2.8.1 version of blast that we have. I have this one parameter that I am confused with. I'm currently trying to produce a tabular output (blastall -m 8 , blastn -outfmt 6), with the parameter -v (Number of database sequences to show one-line descriptions for (V)) for blastall and -num_descriptions in blast 2.8.1 is not compatible with 2.8.1 version of blast with a tabular format. I seem to not understand what exactly this does and how it affects my output. Can anyone help me understand this?

results blast sequence • 346 views
ADD COMMENTlink modified 9 months ago by lieven.sterck6.0k • written 9 months ago by sicat.paolo2030
2
gravatar for lieven.sterck
9 months ago by
lieven.sterck6.0k
VIB, Ghent, Belgium
lieven.sterck6.0k wrote:

outfmt 6, does not provide descriptions summary, so only the -num_alignments is relevant.

The old blastall was a bit more lenient towards those two parameters, the blast+ suite is more strict on it

and I personally prefer -max_target_seqs in tabluar context

ADD COMMENTlink modified 9 months ago • written 9 months ago by lieven.sterck6.0k
2

If you did not see it yet, use -max_target_seqs with causion

https://blastedbio.blogspot.com/2015/12/blast-max-target-sequences-bug.html

ADD REPLYlink written 9 months ago by Bastien Hervé4.4k
1

Thanks for the heads up. My supervisor sent me this https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty833/5106166 to warn me about -max_target_seqs

ADD REPLYlink written 9 months ago by sicat.paolo2030
1

I see, has been extensively discussed in this forum as well

there is a follow-up on that though: from the NCBI blast devs themself (thx @genomax) https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty1026/5259186

ADD REPLYlink written 9 months ago by lieven.sterck6.0k

Hi, Thank you very much for this. This was really helpful and its amazing how the devs explained the issue and resolution simple terms. Thanks!

ADD REPLYlink written 9 months ago by sicat.paolo2030

Thanks. I'm currently being cautious just to make sure I understand each parameter completely. Would -max_target_seq be the same as having both -num_alignments and -num_descriptions?

ADD REPLYlink written 9 months ago by sicat.paolo2030
1

roughly yes.

the only (slight) difference is that -max_target_seqs is summarized per DB entry ID, while -num_alginments is more directly related to the number of HSPs. As such they might, and will, differ if there are multiple HSPs per hit sequence, in that case -max_target_seqs 1 will report all HSPs for that hit sequence , while -num_alignments 1 will only report 1 HSP

ADD REPLYlink written 9 months ago by lieven.sterck6.0k

Thank you very much for the assistance. I think I'll just stick with -num_alignments. Thanks!

ADD REPLYlink written 9 months ago by sicat.paolo2030
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