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6.4 years ago
The Last Word
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I have set of genes and its sequences belonging to an old sequencing experiment. A new geneset has been released for the organism with new gene ids and its sequences. I have BLAST set up to run locally. I am aware that I need to BLAST gene sequences in the old geneset with the new ones so as to know which genes they match to. I am just curious as to what BLAST parameters I should be using. I couldn't find any paper that did something similar. I understand that it should maybe be stringent but how stringent. Can you suggest what parameters you would set for a standalone BLAST in this situation.
I suggest that you use
blastnagainst the latest Apis mellifera genome that you can find here or the transcriptome . Use-task blastn-shortsince you have oligo sequences. Since you are blasting against the same genome you could select only a few top alignments (5).I was thinking to use BLAST against the official geneset OGS3.2 listed here which is built on Amel 4.5. The next part was using the gene names to find their homologoues in the D. melanogaster gene database if possible. Where did you find the transcriptome? I guess BLAST against the transcriptome, getting the gene names and then trying to bind the genenames would also work I guess. However, I would have liked use the beebase ids and convert it into maybe flybase ids.
I liked to NCBI's version of the Amel 4.5 genome where the sequence and transcriptome come from.
also the oligosequences I have are atleast 60 bases in length. I saw online that -short is used in the cases of sequences being less than 50 bases.
You can try without the short directive but if you don't get logical/any results then do the short.
On a different thought, the oligo sequences are probably unique enough that you may be able to do a
grep -wwith them and find the genes they belong to. There may be no need to do blast.Just curious, I should be able to use these oligo sequences to BLAST and find homologous in other species can't I? For using these Apis genes to find homologous genes in Drosophila melanogaster.
If you need to find homologues in other species then I suggest that you find full length sequences first from Bee Genome and then use those for that purpose. That would avoid false positives.
I was using the transcriptiome, so I guess, I will retrieve the full sequences for gene matches and use those. I was thinking that the genome might be a bit too big to really work with it.
can you link me to the page of the transcriptome genomax? I can't seem to find it. Thx
Transcript download link on this page: https://www.ncbi.nlm.nih.gov/genome/48