Basic command-line to run BLAST
...can be found by typing blastp -help break a command up over many lines by using `` to “escape” the new line Blastn blastn [-h] [-help] [-import_search_...2271 days ago
Illumina based assembly pipeline steps !
...ly Primer trimming (Cutadapt; amplicon data only) Choice of multiple assembly tools (SPAdes || Unicycler || minia) Blast to reference genome (blastn) Contiguate assembly (ABACAS...904 days ago
Genome Annotation Transfer Utility (GATU)
...a previously-annotated strain of SARS CoV. This saves researchers from tedious manual annotation of these sequences. The program utilizes tBLASTn and BLASTn algorithms to map genes from...2560 days ago
Taxoblast : Taxoblast is a pipeline to identify contamination in genomic sequence
...e post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence...2382 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example g...sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Colu...Common Name(s), separated by a ';'sblastnames Subject Blast Name(s), se...2165 days ago
Frequent parameters for bioinformatics tools !
...Prokka --usegenus --force --addgenes --rfam --rawproduct cmsearch (taxonomy, 16S) --rfam --noali blastn (taxonomy, 16S) -evalue 1E-10 blastn (MLST) -ungapped -dust...1312 days ago
NCBIBLAST+ 2.14.1 now available
...with the update_blastdb.pl script. And fixed a few bugs related to downloading data from the NCBI, and mt_mode crashing blastn and blastx. Check...276 days ago
BASH script for SelfBLAST a genome
...re sequence to blast" SEQ=$FASTAFILE else echo "Something went wrong $USER - Contact jitendra" fi echo "Doing alignments -- BLASting"; blastn -task megablast -query $SEQ -...2679 days ago
Script to rapid genome clustering based on pairwise ANI
...Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query -db -outfmt '6 std q...dentity flag will speed up the search at the cost of sensitivity: blastn -query -db -outfmt '6 std q...662 days ago
Comment on "Basic command-line to run BLAST"
...BLAST has several different programs that are tailored to different types of queries and databases. The most common programs are blastp, blastn, blastx, tblastn, and tblastx. Choose the prog...450 days ago
Comment on "BLAST+ updated !!!"
blastn [-h] [-help] [-import_search_strategy filename] [-export_search_strategy filename] [-task task_name] [-db database_name] [-dbsize num_letters] [-gilist filename]...2544 days ago