The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) was used as a homology-based method. We performed a Standard Nucleotide BLAST of the RZW genomic DNA using the Highly Similar Sequences (megablast) program in the Expressed Sequence Tags (EST) database for Brachypodium distachyon (taxid: 15368) in order to identify ESTs that correspond to our unknown gene. All matches with greater than 95% Ident were saved. All of the saved ESTs were imported into the CAP3 software. CAP3 generated consensus sequences bases on the overlap between numerous ESTs. To find a full length cDNA sequence for our gene, we performed a Standard Nucleotide BLAST of the RZW genomic DNA using the Highly Similar Sequences (megablast) program in the Nucleotide Collection (nr/nt) database for Brachypodium distachyon (taxid: 15368). We found accession number XM_003562897.4, an mRNA sequence that is predicted to code for the Brachypodium distachyon G-type lectin S-receptor-like serine/threonine-protein kinase B120 (LOC100825184). The two consensus sequences formed were aligned to the cDNA sequence using the NCBI BLAST. To find the official identity of the RZW gene, we performed a Phytozome BLAST search of the RZW genomic DNA with Brachypodium distachyon v3.1 as the target species. The best match to the query sequence was Bradi1g25180.1, and the predicted protein sequence was saved. The FGENESH and Phytozome predicted protein sequences were compared and the working map was updated. From the Phytozome locus page, the functional annotation was saved as a graphic showing domains. The link to Uniprot was followed and there were 16 annotations that contained information about different domains.
Comments
Slight grammatical Issues
Overall very well written--there are just some grammatical issues that popped up that stemmed the flow of the paragraph. Some sentences were very short, which cause the paragraph to sound "fragmented", and more like a list rather than a sequence of events.
Other than that really nothing else to add.
"The National Center for
"The National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) was used as a homology-based method", I don't quite understand this sentence. Is (NCBI) and (BLAST) two different thing or are they the same?
Suggestion
Specify what RZW stands for unless you already did in your introduction. I think there's a typo in the fifth sentence - based instead of bases? You can also add "another" before "standard nucleotide BLAST..." in the sixth sentence if you want, since you did a similar test previously. If you could find a way to shorten that as well it could be beneficial for flow, but it's up to you. Remember to italicize scientific names of species.