I'm working with a phage genome that is 348kb in size. When I try to run a standard BLASTn search, I'm unable to complete the analysis due to the large size of the sequence.
1. What are the best approaches or tools for performing BLAST searches on such large genomes?
2. Are there any specialized BLAST servers or services designed for handling sequences of this size?
3. Would it be advisable to split the genome into smaller segments for analysis? If so, what would be the recommended way to do this?
4. Are there any alternative alignment tools that might be more suitable for this task?
5. What computational resources might be necessary to run a local BLAST on a sequence of this size?
Any advice or suggestions would be greatly appreciated. Thank you!
You can use BLAST+ : https://blast.ncbi.nlm.nih.gov/doc/blast-help/downloadblastdata.html
This is a very small genome which implies that you either have a VERY old computer (pre-2010s), or you are doing something incorrectly. I used to do hundreds of blast searches of whole 40 Mb genomes against other 40 Mb genomes on a pre-2010 MacBook and a given search never took more than a minute.
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