Because I know the identification of my sequence (at the species level), I've discovered that in most situations the BLAST result usually hits the correct species but unpublished sequence. There are two things I am now aware of: (a) Unpublished sequences should not be utilized since there is no guarantee of their validity; (b) If I do not use them, the search for published sequences returns hits with different species in that column. In this case, what should I do?
One more thing, should I use the hits with whole genome, as I have seen that people generally delete those sequences which are generally many folds longer the query sequence (the reason they say is 'it generally cause hindrance in proper alignment? Thanking you in advance...!!
- If the sequence/s are available at NCBI, they can be used in any analysis and would be valid.
- There is no logic of keeping or delete sequence entries based on subject length since blast as its name is a local alignment algorithm and will only look for region similar to the query.
Hi
First of all the answer to this question depends a lot upon your research question, in general as suggested by Abhijeet Singh you can use any sequence available at NCBI if they are your BLAST hits. If I was you I will pay attention to the selection of species and sequences based upon my query of concern. In terms of your hits with whole-genome sequences, it is quite natural given BLASt uses local alignment which searches similarities throughout its database, and any stretch of sequence which matches your query will be returned as a possible hit. So pay attention to query coverage and identity too. Hope this helps.
Cheers
Pankaj
Hi Vinay. For your phylogenetic analysis, I recommend using sequences from perfectly characterized organisms and, if possible, belonging to institutional collections, instead of using those of BLAST result. In the case of microorganisms, there are collections such as CBS, ATCC, BRIP, etc., which have numerous and very useful records.
Thank you, Abhijeet sir, Pankaj sir and Karla mam for your kind suggestions.
- Dear Vinay, If you are a taxonomist then select only the published sequences which are available at NCBI, because some persons (other than taxonomist) BLAST the sequence and find the some matches related his sequence then he named the his sequence as the blast search match name, so please aware from this type of nomenclature
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