BLAST plus: architecture and applications. BMC Bioinformatics. 2009;10:421. Article PubMed PubMed Central Google Scholar Wu T, Hu E, Xu S, Chen M, Guo P, Dai Z, et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb). 2021;2:100141. ...
This strategy is conceptually similar to the popular tools like BLAST [39] for sequence alignment or our previous strategy scLearn et al. for automatic cell type annotations using single-cell transcriptomic references [24, 25, 30]. In the case of SpaDo, it performs a search by measuring the...
For each putative site, we sorted the pool of BLAST hits by subject strand (in this case, “subject” refers to our plant reference genome) to find which of the paired reads were associated with either the plus or minus strand. Because the transgene-containing end of the amplicon is closes...
While some previous methods also align to the virus first [97], either the software no longer appears available where specified at publication [98, 99], or they use BLAST [100, 101] instead of a faster short read aligner [102]. Unlike ViFi [58], Polyidus requires that the chimera ...
Phytophthora root rot caused by the oomycete Phytophthora capsici is the most devastating disease in pepper production worldwide, and current management strategies have not been effective in preventing this disease. Therefore, the use of resistant variet
Detailed workflow of the three annotation servers, KAAS, MEGAN4, and MG-RAST using query sequences after gene finding process of sequenced data; KAAS and MEGAN4 use BLASTP and BLASTX for amino acid and nucleotide query sequences respectively and the MG-RAST uses only BLASTX. All use differe...
n=3, NC: Normal control Full size image Discussion IT is well established that blastema formation results from the dedifferentiation of the differentiated cell types on the amputation plane back to embryonic-like cells (Mescher 1996), but these cell types retain the memory of their origin when ...
Sequence based identification and annotation of Affymetrix probesets[http://mriweb.moffitt.usf.edu/mpv/share/MPV_U133PLUS_Export.zip] Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search program...
[81,82]. Potential homologs to these proteins were identified inDesulfuromusasp. GH17 by BLAST using query proteins for NSR and NSR-like proteins from S0-reducersPyrococcus furiosusandThermovibrio ammonificansas well as Sre/Psr genes from a variety of bacterial taxa (complete output and list of...
(Additional file2: Fig. S6). One introgression occurred betweenC. fugongensisand the ancestor of the japonica-corniculata clade plusC. fugongensis, with a BS value of 84%, where the ancestor contributed 23.6% of genetic material toC. fugongensis(Fig.3e). It is worth noting that such ...