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6.6 years ago
raber82
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I am trying to find a gene inside a whole genome of Fungi which is consist of (32500 gene) .. But I have a sequence of that gene from bacteria only,,,, Is there anyway I can scan the whole genome to find the sequence or even near sequence of that bacterial gene ??? Please any help or direction would be really appreciated.
did you search COGs and KOGs for this gene? If it is part of a pathway, you can search in KEGG for orthologous genes.
I am not so familiar with these, But up to now , I could be able to split the genome based on the size,,, The gene in bacteria is arround 1700 bp ,, I collected all genes that are between 1700 - 1800 in one fasta file....
I need just to Align the bacteria gene as a reference with all fasta file to find the similarity between them...
So I have control sequence , I need to compare every gene sequence with it automatically, to find the similarity rate...
IS there any software doing so Thanks alot for your reply
If fungal genome is available in NCBI/ENSEMBL or any other public genome server that offers BLAST, blast your bacterial gene sequence against fungal genome. You will be able to get nearest match.
If my understanding is correct, you have collected gene sequence with 1700-1800 bp length from reference (fungal) genome (in one fasta file) and you have query sequence (bacterial) in another file (fasta format, probably). Then you can use tools such as standalone blast tool from NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download). This approach has a problem that orthologous gene (in fungus), may or may not be of same length of bacterial gene.
I would suggest to go with first approach if reference (fungal) genome is hosted on a server that supports blast.