Hi everyone,
I am trying to find any infromation how to extract the known cordinates from the genbank file but had no luck so far.
This is how i have my results where the top line is the chromosome and from each chromosome I want to extract the sequence from the given cordinates.
gnl|BL_ORD_ID|21 CM017728.1 Coilia nasus isolate PX2019 linkage group LG22, whole genome shotgun sequence
9825652 9826524
9854872 9855648
9866528 9867421
gnl|BL_ORD_ID|14 CM017720.1 Coilia nasus isolate PX2019 linkage group LG15, whole genome shotgun sequence
28861074 28862216
gnl|BL_ORD_ID|23 CM017730.1 Coilia nasus isolate PX2019 linkage group LG24, whole genome shotgun sequence
9828100 9829197
14400268 14401302
16620220 16621236
If anyone knows where i can find some documentation, example of how to do it, I would be really greatful!
3 answers
get your data as FASTA instead of GenBank then you can extract sequences from it in different ways
wherever you get GenBank usually you can get FASTA files as well. You can also covert GenBank to FASTA with various tools, you could use the bio package see: https://www.bioinfo.help/ to transform into fasta
bio fetch NC_045512 | bio fasta > genome.fa
now index the FASTA file:
samtools faidx genome.fa
and after that, you can extract any subsequence of it with
samtools faidx genome.fa NC_045512.2:100-120
prints:
>NC_045512.2:100-120
CGGCTGCATGCTTAGTGCACT
Using EntrezDirect (truncated to save space) :
$ efetch -db nuccore -id CM017728.1 -seq_start 9825652 -seq_stop 9826524 -format fasta
>CM017728.1:9825652-9826524 Coilia nasus isolate PX2019 linkage group LG22, whole genome shotgun sequence
TCGCTCTGTTGTGTTTTTGCCCCAAATGGCTCGGTAGCACTTGGGTACAAGGAGACAGAATATGATGCCG
TAGTTGGAGACCAGGATGGCGGAGGCCTGTACAATGGGGCGAGACTCGTTCCTGGTGATGTAGATAGGAA
Use following additional options when applicable.
-strand 1 = forward DNA strand, 2 = reverse complement
(otherwise strand minus is set if start > stop)
-forward Force strand 1
-revcomp Force strand 2
"Slicing" out regions of a Genbank is super easy with Biopython:
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