blast culling_limit option behavior
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4.4 years ago
erwan.scaon ▴ 820

I am using culling_limit 1 as a parameter

From the manual : Delete a hit that is enveloped by at least this many higher-scoring hits

My understanding : The culling limit can be used to remove redundant hits. In practice it sets the number of hits returned per subject sequence

The command line $blastn -query reads.fa -subject locus.fa -strand plus -culling_limit 1 -dust no -out result.csv -outfmt 6

One unexpected result : qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore QJLFG:08700:06611 gi|372099098:113208001-113426000 98.131 107 1 1 1 106 51978 52084 5.11E-49 185 QJLFG:08700:06611 gi|372099098:113208001-113426000 79.167 120 14 8 103 215 217412 217527 4.15E-15 73.1 QJLFG:08700:06611 gi|372099098:113208001-113426000 97.561 41 1 0 103 143 217437 217477 1.49E-14 71.3

The "3rd hit" as far as i understand is redundant regarding the "2nd hit" : same subject region, same part of the read involved, but it's a shorter alignement with a higher e-value

Why is it not discarded with culling_limit 1 ?

blastn culling_limit alignment • 3.0k views
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Entering edit mode

Hum it's pretty hard to read, here is a focus on relevant infos :

format : qstart<->qend --- sstart<->send --- evalue

2nd hit : 103<->215 --- 217412<->217527 --- 4.15E-15

3rd hit : 103<->143 --- 217437<->217477 --- 1.49E-14

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