I'm carrying out a gene expression study (mRNA seq) of a gene, I noticed the BLAST results of the gene from species with same family had higher variations, but on aligning to the reference genome of the family species the variation was very less. Can I use the whole genome region that aligned with my gene of interest to comparative? rather than using the BLAST search gene sequences that had higher variations.
Have you tried using the filter for species when using BLAST? You may want to compare the template sequence without introns as those gaps would have a negative impact on the BLAST score. Overall it is possible to align reads against a template genome but you should use a tool like Artemis to do so.
Yeah I have been able to use filter in the blast search, and had result of specific specie sequence of choice. I have never used Artemis for sequence alignment, will give it a try here. Thank you @Robert Adolf.
What kind of organism you are studying ?
Eukaryotes have introns and prokaryotes do not have.
This is important for bioinformatic algorithm.
In some species coding part (exons) are small part from whole gene (long introns). I am afraid that without introns you can not find the gene in whole genome. Program algorithms are adjusted to find the most longer and exact alignment between sequences. If you have short exons and long introns, there is not a way to found position of this gene in genome. You can tray to find one by one exons. Good luck !!! :-)
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