I am trying to find out how many copies of a gene that I have primers for are in a training set of genomes. I would like program where I enter the genome and the primer (that has degenerate bases) sequences and it finds the primer sequence for me in the genome. Does such a program exist? For free? BLAST didn't seem to work, as it will find just part of the primer sequence and give too many hits.
- This question is misleading a bit. I would suggest you to not look for copy number of gene based on primer sequences.
- Simplest would be, and if they are training genomes, they should be annotated. If they are annotated, the copy numbers of genes are readily available.
- Primer sequence is designed from the gene sequence, however, degenerate primers are not covering everything anyway.
- Blast can still be used if the parameters for the output is adjusted if you really want to do based on primer sequences, but it is not preferred in my opinion.
Jennifer Hathaway To match the two sequences, you can use ClustalW multiple alignment approach. However, as suggested by Abhijeet Singh , this can not be the approach to know the gene copy number in particular genome. However, if you want to be sure whether these primers would not give you any non-specific amplification, you can check it as suggested using ClustalW.
Jennifer Hathaway To match the two sequences, you can use ClustalW multiple alignment approach. However, as suggested by Abhijeet Singh , this can not be the approach to know the gene copy number in particular genome. However, if you want to be sure whether these primers would not give you any non-specific amplification, you can check it as suggested using ClustalW.
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