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9.3 years ago
sharma_tina189059
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50
Hello,
I have got 1500 contigs of a fungus from ncbi. I want to find out genes of my interest. For which I have 21 fully annotated gene description. Can anyone suggest me the initial in silico step for annotating these contigs?
Hi,
Do you mean that 21 are the description only without any sequences? If yes, I suggest you to use the description in Entrez and get corresponding sequences for each description. Then you can use HMMER (or even BLAST) to search against your 1500 contigs. Set some parameter to accept only significant result. One you get the hit, you might double check it with gene enrichment analysis such as Gene Ontology.
Hope this helps.
No, I mean complete description having sequence as well in a database.
Simple blast between gene sequences and contigs could tell you whether those genes are there are not. If you want to annotate all contig, predict genes using augustus and do the blast against fungal database to get homologues.
Have you checked if this species is available in fungi.ensembl.org?
No, it is not available in ensembl.org.
Ok, if the full genome is not yet available (in GenBank, ENA) have you thought in trying MAKER?