Results for "blastn"
Blogs
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_...2245 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...878 days ago
Bookmarks
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...2534 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...2356 days ago
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Top-level pages
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...2140 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...1287 days ago
Wire posts
News
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...250 days ago
Bio-Scripts
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 -...2653 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...636 days ago
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Tags
Converting BLAST output into CSV
Suppose we wanted to do something with all this BLAST output. Generally, that’s the case - you want to retrieve all matches, or do a reciprocal BLAST, or something. As with most programs that run on UNIX, the text output is in some specific format. If the program is popular enough, there w...Tags: Convert, BLAST, output, CSV, blastn, megablast
2338 days ago
Understanding BLASTn output format 6 !
BLASTn output format 6 BLASTn maps DNA against DNA, for example gene sequences against a reference genomeblastn -query genes.ffn -subject genome.fna -outfmt 6 BLASTn tabular output format 6 Column headers:qseqid sseqid pident length mismatch gapopen qstart qend sstart send eva...Tags: BLASTn, blast, alignment, output, format, 6
2140 days ago
Comments
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...424 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]...2518 days ago
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