Retrieve amino acid sequences from old locusID?

Question

[taylrtam]

Hi,

I have a list of discontinued locusID tags that I want to retrieve the amino acid sequences for.

The list is as follows:

Bphyt_0466

Bphyt_4414

...

Bphyt_4439

Is there any way to batch retrieve the amino acid sequences?

Answer 1

[Sparrow_kop]

Hi, you can use R 'KEGGREST' library to extract the amino seq from the KEGG database: The below is the demo script:

library(KEGGREST)
library(Biostrings)

aaseq_query <- keggGet("bpy:Bphyt_2906", "aaseq")
aaseq <- as.character(unlist(aaseq))
aaseq

[1] "MSEKEIDQVLVERVQKGDKAAFELLVSKYHRKILRLISRLVRDPAEVEDVAQDAFIKAYRALPQFRGESAFYTWLYRIAVNTAKNYLATQGRRAPTSTEADAEEAETFSDADQLRDINTPESMLMSKQIAETVNAAMAVLPEELRTAITLREIEGLSYEEIAEMMGCPIGTVRSRIFRAREAIAAKLRPLLDTPEGKRW"

The other way is to use web scrapping by python or others, use the below url :

http://www.genome.jp/dbget-bin/www_bget?bpy:Bphyt_2906

and you can replace the gene id at the last position in the url , and the write a script to parse the web to extract the seq.

Answer 2

[Sparrow_kop]

Hi, you can use R 'KEGGREST' library to extract the amino seq from the KEGG database: The below is the demo script:

library(KEGGREST)
library(Biostrings)

aaseq_query <- keggGet("bpy:Bphyt_2906", "aaseq")
aaseq <- as.character(unlist(aaseq))
aaseq

[1] "MSEKEIDQVLVERVQKGDKAAFELLVSKYHRKILRLISRLVRDPAEVEDVAQDAFIKAYRALPQFRGESAFYTWLYRIAVNTAKNYLATQGRRAPTSTEADAEEAETFSDADQLRDINTPESMLMSKQIAETVNAAMAVLPEELRTAITLREIEGLSYEEIAEMMGCPIGTVRSRIFRAREAIAAKLRPLLDTPEGKRW"

The other way is to use web scrapping by python or others, use the below url :

http://www.genome.jp/dbget-bin/www_bget?bpy:Bphyt_2906

and you can replace the gene id at the last position in the url , and the write a script to parse the web to extract the seq.