BLAST is a powerful tool for analyzing biological sequence data.Since the initial release of BLAST in 1990, it has undergone continuous updates to improve its speed and accuracy. BLAST is now considered a crucial and widely used tool in the field of bioinformatics. It has played a vital role ...
We next compared OnClass with methods that can reject cells to all seen cell types, including sCN(reject), LR(reject), SVM(reject), Cell BLAST(reject), and DOC(reject). However, these methods can only group the rejected cells into a generic “unknown” type. To the best of our knowled...
EST database search Nucleotides from 1 to 500 of the human transposon L1.2 (GenBank accession no. M80343) were used to search for LINE-1 chimeric transcripts in the human expressed sequence tag (EST) database (GenBank) by using the BLAST (Basic Local Alignment Search Tool) program. To ...
Transcripts were annotated using BLASTN and BLASTX (NCBI) searches. Trial experiments with a reduced stringency (2 fold enrichment) proved to yield many transcripts not selective for the mesopallium in ISH experiments. In contrast, 3-fold enrichment was too stringent, excluding mesopallium-...
Identification of CRISPRs was performed using MinCED (https://github.com/ctSkennerton/minced) and default options. Spacer sequences were retrieved and searched in archaeal MAGs from Lake Dziani Dzaha with blastn [59] (options “blastn-short” and “qcov_hsp_perc 80”, allowing to retrieve ...
Identification of CRISPRs was performed using MinCED (https://github.com/ctSkennerton/minced) and default options. Spacer sequences were retrieved and searched in archaeal MAGs from Lake Dziani Dzaha with blastn [59] (options “blastn-short” and “qcov_hsp_perc 80”, allowing to retrieve ...
In this manuscript, a pairwise-sequence-similarity based approach (using the bioinformatics tool CLANS) is used to analyze all available central Hox protein sequences. The results are combined with a large-scale species phylogeny to depict the presence/absence of central Hox sequence-types across ...
Further- more, we compared the Arabidopsis protein sequences against cucumber unigenes using the blast program with an e-value cutoff of 1e-10 and found that ~67% of all the Arabidopsis protein sequences had at least one matching cucumber unigene. Microarray analysis in Arabidopsis indicates ...
We analyzed these genomic sequences by BLAST to localize the cruzipain sequences in both genomes. We manually annotated the target sequences to establish the localization of all cruzipain sequences and their flanking genes. To do so, we compared our genomic sequences with annotated T. cruzi ...
Table 2 Second-order match homology analysis of query genes in the genomic island using the BLASTn module forErwinia amylovoraATCC49946. Full size table These results suggest that GI may be horizontally transferred from theEnterobacteriaceaepathogens toE. amylovora. In a previous study of the gen...