Question: Obtaining all comparisons of a query
0
gravatar for martinianodl
3.1 years ago by
martinianodl0 wrote:

Hello,

I am trying to retrieve the rank from all comparisons made from a query. For example:

  • I have a database with 10,000 elements.

    • >gi|1705556|sp|P54670.1|CAF1_DICDI RecName: Full=Calfumirin-1; Short=CAF-1 MASTQNIVEEVQKMLDTYDTNKDGEITKAEAVEYFKGKKAFNPERSAIYLFQVYDKDNDGKITIKELAGDIDFDKALKEY KEKQAKSKQQEAEVEEDIEAFILRHNKDDNTDITKDELIQGFKETGAKDPEKSANFILTEMDTNKDGTITVKELRVYYQK VQKLLNPDQ
  • I am querying the five first elements of the protein that is on the database (I am doing that for all the elements):

    • MASTQ

I would like to know in which position the right comparison is, for example 14th out of 10,000.

The commands I'm using provide me different lists of hits found. For first query 77 hits, for second query 255 hits and so on.

Is there any way to BLAST return me a list with all the comparisons made? even the ones with score 0 (zero)?

If it's not possible, why it can't be done?

I am using the blast 2.4.0+ and the command: blastp -num_threads 8 -query query.fa -db db/blast/irish -max_target_seqs 10000 -outfmt "6 qseqid sseqid evalue bitscore"

Any advice would be greatly appreciated.

blast alignment • 868 views
ADD COMMENTlink modified 3.0 years ago by Biostar ♦♦ 20 • written 3.1 years ago by martinianodl0

Tell me if I am getting this right: You are not interested in the blast per se but only want to see if the "subject" protein starts with MASTQ? Why is the position of that hit important in the blast result?

ADD REPLYlink written 3.1 years ago by genomax75k

Actually I want to compare for example the first five elements of the protein with the whole database, get a ranking list with the score of each comparison and do that for all the elements on the database. I want to do that for the 5th, 6th, 7th, n-th element until I find the minimum number of elements that will give me the "best overall score" (where most of the comparisons were correct).

So, basically I want to query each element of the database against the rest of it and find the minimum number of elements I need to have an accurate query.

The position is important to me because I want to compare the blast results with my algorithm.

Thanks in advance

ADD REPLYlink written 3.1 years ago by martinianodl0
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