Hey Folks,
Background:
I am trying to shortlist the list of genes predicted by different gene prediction methods. For this i am considering blast hits as my basis for shortlisting.
I merged the results obtained from different gene prediction methods as follows:
AB_Contig140_G3 Start end
ABC_Contig131_G47 Start end
ABC_Contig67_G20 Start end
where A, B, C stands for gene prediction methods. For example g3 with coordinates start and end in contig 140 was found in gene prediction methods A and B.
Question:
Blast: i am using a large database to blast my genes against it and i want only the best hit(Say 1 or 2) to just confirm that the gene predicted by gene prediction methods is actually a good gene with a good score.
I have tried to use various flags for blast commands as follows:
1) Command:
blastn -query gene_Seq_22471 -out 24712_trial0.blast.txt -db Fastadb -outfmt 6
output: 17 hits
ABC_Contig7_G17 gi|385856165|ref|NC_017518.1| 100.00 924 0 0 1 924 1523212 1524135 0.0 1707 ABC_Contig7_G17 gi|385340991|ref|NC_017514.1| 100.00 924 0 0 1 924 812018 811095 0.0 1707 ABC_Contig7_G17 gi|254804028|ref|NC_013016.1| 100.00 924 0 0 1 924 1364185 1365108 0.0 1707 ABC_Contig7_G17 gi|385339062|ref|NC_017513.1| 99.78 924 2 0 1 924 1412253 1413176 0.0 1696 ABC_Contig7_G17 gi|385852231|ref|NC_017516.1| 99.68 924 3 0 1 924 822476 821553 0.0 1690 ABC_Contig7_G17 gi|385850283|ref|NC_017515.1| 99.68 924 3 0 1 ...