Question: How to interpret the SeqIO.parse record for GenBank features?
gravatar for jolespin
3.8 years ago by
United States
jolespin130 wrote:

I'm calling these attributes of the feature class: feature.location, feature.type, feature.strand

from the record.features in SeqIO.parse(gbk_file,"genbank")


[0:6183918](+) source 1
join{[1871:2015](-), [1776:1872](-), [1751:1775](-), [1419:1752](-), [1304:1418](-), [1051:1303](-), [810:1050](-), [722:809](-), [634:721](-), [336:633](-)} CDS -1
[2126:2723](-) CDS -1
[2674:2959](-) CDS -1
[2906:3869](-) CDS -1

I know the (-1) goes with the (-) strand and (1) with the (+) strand.

Is the slice object referencing the (+) strand even when the feature is on the (-) strand? In other words, the 3rd entry, is [2126:2723] on the + strand but the reverse-complement is the feature OR is it in relation to the opposite end of the strand?

Also, what is going on with this join object?

ADD COMMENTlink written 3.8 years ago by jolespin130
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 962 users visited in the last hour