I have assembled transcriptomes of various invertebrate species. I would like to confirm the species from which the sequence data was sources.
I have been using cytochrome-c oxidase subunit 1 (COX1) as a BLAST query, then putting the top hit of that BLAST back into NCBI to see what species is the closest match. However, in only about 1 in 5 cases does NCBI return the correct species. It sometimes gets the correct genera, but sometimes not even the genera is correct...
I thought that COX1 sequences would provide a precise match and allow unambiguous identification (at least, for species that have COX1 on NCBI). Is there a better way of identifying species from sequence information?
Many thanks for your help.
Hi Al! also depends on the group of organisms you are working with. Are they arthropods? You might want to check what other genes are used for "barcoding" the group you are working on.
You can use sequences from BOLD as reference and add phylogenetics inference.