SB Blast 2 seqs - mendessoares/BuddySuite GitHub Wiki

--bl2seq, -bl2s

Description

Perform an all-by-all blast among sequences, using the blast2seq method. The results are returned as a tab delimited list of the top hit from each sequence pair (if any), and the headings include %ID, hit length, E-value, and bit-score. No sequences are returned.

Example

Input file: Drosophila.nex

#NEXUS
begin data;
    dimensions ntax=4 nchar=316;
    format datatype=protein missing=? gap=-;
matrix
'Dme-Panxδ1' YKLLGSLKSYLKWQIQTDNAVFRLHNSFTTVLLLTCSLIITATQYVGQPISCIVGVP-HVVNTFCWIHSTFTMPDRREVHPGVDF-KYYTYYQWVCFVLFFQAMACYTPKFLWNKFEGGLMRMIVGLNITRKRDALLDYLIKHVKRHKLY-AYWACEFLCCINIIVQMYLMNRFFDGEFLSYGTNIMKLSDVPQEQRVDPMVYVFPRVTKCTFHKYGPSGSLQKHDSLCILPLNIVNEKTYVFIWFWFWILLVLLGL--VFRCIIFPKFRPRLLNASNRIPMECRLDIGDWWLIYMLGRNLDPVIYKDVMSEFQVP
'Dme-Panxδ2' MDVFGSVKGLLKIDQV-DNNVFRMHYKATVIILIAFSLLVTSRQYIGDPIDCIVEIPLGVMDTYCWIYSTFTVPEGRDVQP--GSEKYHKYYQWVCFVLFFQAILFYVPRYLWKSWEGGRLKMLVDLSVNDKDRKIVDYFG-NLNRHNFYAFFFVCEALNFVNVIGQIYFVDFFLDGEFSTYGSDVLKFTELEPDERIDPMARVFPKVTKCTFHKYGPSGSVQTHDGLCVLPLNIVNEKIYVFLWFWFIILSIMSI-SLIYRIAVAPKLRHLLLRARSRAESEVEVAIGDWFLLYQLGKNIDPLIYKEVISDLEMG
'Dme-Panxδ3' -----GFI---K----IDNMVFRCHYRITAILFTC-CIIVTANNLIGDPISCI--IPMHVINTFCWITYTYTV---A--GPGLE-K--HSYYQWVPFVLFFQGLMFYVPHWVWKM-D-GKIRMITG--VDDRDRIL-KYFVNNT--HNGYSFYFFCELLNFINVIVNIFMVDKFLGGAFMSYGTDVLKFSNMDQ-DRFDPMIEIFPRLTKCTFHKFGPSGSVQKHDTLCVLALNILNEKIYIFLWFWFIILATISGVAVLYSVVI---TR-TIR----------K--EGDFLILHFLSQNLSTRSYSDML-Q----
'Dme-Panxδ4' MAAVKPLSKYLQFKVHIYDAIFTLHSKVTVALLLACTFLLSSKQYFGDPIQCF-G-D-KDMDAFCWIYGAYL-QCAVSK--VVEN--YITYYQWVVLVLLLESFVFYMPAFLWKIWEGGRLKHLCDFKRTHRV--LVNYFETHFR----YFVYVFCEILNLSISILNFLLLDVFFGGFWGRYRNALY-------NQWI-AV---FPKCAKCEYKG-GPSGSSNIYDYLCLLPLNILNEKIFAFLWIWFI-LAMLISLKFLYRLAVLYPMRLQLLRPKKHLQVALNCSFGDWFVLMRVGNNISPELFRKLLEEL---
;
end;

Usage example

$: sb Drosophila.nex -bl2s

Output

#query	subject		%_ident	length	evalue	bit_score
Dme-Panxδ3	Dme-Panxδ1	42.32	293	2e-77	228
Dme-Panxδ2	Dme-Panxδ1	50.48	311	1e-119	338
Dme-Panxδ4	Dme-Panxδ1	30.79	302	1e-50	159
Dme-Panxδ4	Dme-Panxδ2	37.99	308	2e-67	204
Dme-Panxδ3	Dme-Panxδ2	48.46	293	4e-91	263
Dme-Panxδ4	Dme-Panxδ3	32.75	284	3e-43	138