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. ...
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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...
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 ...
based on a similarity search against a reference database such as the NCBI-NR database of non-redundant protein sequences [1], usually employing a variant of the BLAST program [2], or on the protein domain search against a protein family database such as PFAM [3]. This is mainly ...
2009, 10: 25-10.1186/gb-2009-10-3-r25. Article Google Scholar Kent WJ: BLAT – the BLAST-like alignment tool. Genome Res. 2002, 12: 656-664. 10.1101/gr.229202. Article published online before March 2002. Article PubMed CAS PubMed Central Google Scholar Dobin A, Davis CA, ...
Transcripts that were differentially expressed between cutting-stress samples and control samples were detected by using a G-test with a false discovery rate threshold of 0.1%. The Sb04g024710 gene sequence was aligned to genes from Phytozome and Cufflinks by using BLAST + version 2.2.26[24...
MDS, especially high-grade MDS, has a high risk of transformation to a secondary AML [17]. MDS is the most common adult myeloid malignancy, has a blast count < 20%, and in about 30% transforms to AML, termed “secondary AML to MDS” or bone marrow failure. According to the Inte...
by the product of the bi-directional blast hit scores from A. niger versus T. reesei homology search used to construct the model. Path lengths from 3 to 12 were investigated. The p-value of a path was estimated from an empirical distribution of shuffling the edge and node weights 10 000...