Question

Can I easily download the LOC... numbers of the genes of my peptide sequences?

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2.7 years ago

ysf.cyln • 0

Can I easily download the LOC... numbers of the genes of the peptide sequences? Anyone know about this? Or should I do it by entering the XP codes one by one?

Gene LOC Peptid • 1.1k views

ADD COMMENT • link updated 2.7 years ago by GenoMax 141k • written 2.7 years ago by ysf.cyln • 0

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Provide examples of XP id's and I can possibly show you one way.

ADD REPLY • link 2.7 years ago by GenoMax 141k

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XP_021978004.1 XP_021981154.1 XP_021981634.1 XP_021982728.1 XP_021982746.1 XP_021983621.1

they are some example XP codes.

ADD REPLY • link 2.7 years ago by ysf.cyln • 0

score 1 · Answer 1 · 2021-08-31

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2.7 years ago

GenoMax 141k

Using Entrezdirect:

$ for i in `cat id`; do printf "${i}\t"; esearch -db protein -query ${i} | elink -target gene | esummary | xtract -pattern DocumentSummary -element Name; done
XP_021978004.1  LOC110873394
XP_021981154.1  LOC110877312
XP_021981634.1  LOC110877745
XP_021982728.1  LOC110878680
XP_021982746.1  LOC110878702
XP_021983621.1  LOC110879465

id file contained your identifiers. One per line.

ADD COMMENT • link 2.7 years ago by GenoMax 141k

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I can get their LOC number from gene search. Can i get them easily? u know?

ADD REPLY • link 2.7 years ago by ysf.cyln • 0

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See updated answer above.

ADD REPLY • link 2.7 years ago by GenoMax 141k

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Yes, i saw. Did you use a program like R or from NCBI?

ADD REPLY • link 2.7 years ago by ysf.cyln • 0

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From NCBI. It is linked above.

ADD REPLY • link 2.7 years ago by GenoMax 141k