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...
Firstly, the miR-483-5p sequence was subjected to a sequence alignment using the National Center of Biotechnology Information (NCBI) blast tool against the IGF2/H19 enhancer (NG_042039.1), revealing potential binding sites of miR-483-5p within the IGF2/H19 enhancer region (2 to 8 bases in...
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...
BlastP is then used to relate the resulting amino acid sequences to a protein database. The ORF from each transcript with the best hit to the database is then selected as the predicted true ORF. Using the ORF information, the transcripts are then labeled with attributes based on the ...
(1).It is worth noting that within 30 core ASVs, there are ASVs that were assigned similar phylogenies even though they have different sequences. BLASTn analysis of these sequences has revealed that sequences vary in identity (96 to 100%) and coverage (90 to 100%). Based on this ...
48. “Deep” from ‘Ten – Redux’ (1991/2009) Share ‘Ten’ is a classic album with not an ounce of fat on it, but ‘Deep’ is one song that could qualify as a, ahem, ‘deep track.’ It’s one last blast of intensity before ‘Ten’ wraps with ‘Release.’ Some fans have ...
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 ...
Additional file 3: Supplementary materials and methods. (PDF 18 KB) 12859_2008_2721_MOESM4_ESM.pdf Additional file 4: Details of regular expression and HMMER profile search-derived mouse PTS2 candidates after triage and annotation plus comparison with PeroxisomeDB PTS2 Predictor Blimps Search. (PD...
[http://link.springer.com/chapter/10.1007%2F3-540-45014-9_1] Chapter Google Scholar Johnson M, Zaretskaya I, Raytselis Y, Yuri Merezhuk SM, Madden TL: Ncbi blast: a better web interface. Nucleic Acids Res 2008, 36(2):W5-W9. doi:10.1093/nar/gkn201. doi:10.1093/nar/gkn201. ...