Gene ontology from annotation
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4 weeks ago
jaqx008 ▴ 110

Hello, I am needing some help identifyng the GO of a gene. I have a cordinate for the gene, I just need to find its GO using the loci info. Is that doable?

function non-model animal GO gene • 273 views
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Do you have an organism or all you have is just a coordinate? ... :-) (ok, ok I am just being faceitous)

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:) Yes I have an organism. Lancelet.

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The genome annotation for Branchiostoma lanceolatum is in Ensembl Metazoa: https://metazoa.ensembl.org/Branchiostoma_lanceolatum/Info/Index

In case that is your organism, Ensembl Metazoa has already done the annotation for you, just pick your gene id and go (example annotation). No need to install anything.

The genome of Branchiostoma floridae (Florida lancelet) is in GenBank/RefSeq. Here is the entry to the NCBI taxonomy for lancelet which links to all sequences available for this taxon.

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4 weeks ago

Once upon a time, one could simply download a blast-database (or so I remember, maybe a fasta file) and then we could simply blast vs. GO. For whatever reason, this is not available anymore, but I found this: https://github.com/Duke-GCB/MMAP-Docker/tree/master/makeblastdb-go

This is a script to download sequences and create a blastdb on the fly, I haven't tried it, but looks promising. If you have a lot of genes to annotate, this is certainly an option. Another option is to use InterProScan that can also give you GO annotations. These are based on protein families and domains. In my experience these terms are slightly different (in a good way) from what you get by pure blast searches. They are more "conservative" than e.g. blas2go terms, that means you get less, but those ones you get are normally specific (blast2go also assigns top level or high level terms like "biological process" which are not informative) and more reliable. In order to annotate whole genomes, it is recommended to use a local installation of InterProScan.

Another commercial tool that come to mind are Blast2GO, the free test version should definitely get you an annotation, but for a single gene both methods might be overkill.

If you know the gene name/symbol, try AmiGO gene search. If you have the sequence only, run blast in UniprotKB (or local blast vs. SwissProt) and extract whatever GO terms come up there.

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Great tips. I think one of this will give me what I am looking for. Thanks a bunch

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4 weeks ago

Get the sequence for your gene, find the most similar annotated genes (from other, annotated organisms) then evaluate whether the similarity is sufficiently high to assume that the gene has similar functions.

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While I have done this before, I am trying to use the GO to perform functional analysis to determine like biological function, with a tool like blast2go. I am not just trying to know a probable function.

Thanks for your suggestion tho

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