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multi species_gene name to description

Dear colleagues,

I have a large set of gene names that belong to the "multiple species". I am wondering if you are aware of any pipeline that can print the description of the genes based on their names? To the best of my knowledge, the majority of the pipeline mentioned on the community require the explicit selection of the "reference species" and mainly perform enrichment analysis. The question in my case is only the description.

Example toy data look like:

EF1A_CHICK, PPN_DROME, RL8_DANRE

Thanks in advance

gene function transcriptome
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updated by GenoMax GenoMax • written by Phismil • Phismil

2 answers

Have a look at UniProt. It contains multiple functional information (amino acid sequence, name or description, GO etc). Here is an example of it's functionality with the toy data you provided. You can add more columns by editing "columns" tab.

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written by Shalu Jhanwar Shalu Jhanwar

Using EntrezDirect:

$ more test
EF1A_CHICK
PPN_DROME
RL8_DANRE

$ for i in `cat test`; do printf ${i}"\t"; esearch -db protein -query ${i} | esummary | xtract -pattern DocumentSummary -element Title; done
EF1A_CHICK      RecName: Full=Elongation factor 1-alpha 1; Short=EF-1-alpha-1; AltName: Full=Elongation factor Tu; Short=EF-Tu
PPN_DROME       RecName: Full=Papilin; Flags: Precursor
RL8_DANRE       RecName: Full=60S ribosomal protein L8
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written by GenoMax GenoMax

Thank you for your reply!

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written by Phismil • Phismil

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