$begingroup$ I have downloaded the BLAST formatted nt database from and i am seeking to extract sequences using an accession number list acquired with esearch and efetch. Nonetheless, This is often causing a big number of surprising sequences, my final results contain entire genomes whilst my list of accession numbers only contains shorter sequences.
states the reference genome is extremely fragmented, but there is no explanation about how the OP established this). I believe that the N50 worth might be handy, but I need some context to know precisely what is "very good" or "undesirable". I am in a lack of where by to get started on, so any details will probably be enormously appreciated! -Leah
$begingroup$ what is among the most exceptional search term look for query to enter into NCBI So that you can locate all the obtainable proteins accession numbers for a selected loved ones?
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When evaluating final results acquired when examining sequencing info applying these databases, I discovered a strange boost in the number of reads assigned on the Leishmania chagasi species (that is a terminal node mobile number database free download during the taxonomy for the two databases) when going from db2 to db3.
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To elucidate a little more, unique reads are assigned to some taxon depending on the kmer assignments for that browse (i.e. Each and every kmer in just a browse primarily votes with the read taxon). The behaviour of assignment immediately after altering the database is unpredictable at a read degree since the kmer assignments will improve.
HMMR is an additional excellent choice. But that's a complete diverse problem and we'd need the exact Organic concern you are trying to answer to have the ability to guidebook you there. This Instrument, however, is the commonest and simplest way I realize to blast against the varied typical DBs from your neighborhood equipment.
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