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):
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.