Results for "blastn"
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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_...2237 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...870 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...2526 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...2348 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...2132 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...1279 days ago
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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...243 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 -...2645 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...628 days ago
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Basic command-line to run BLAST
The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before. All of the commands below can copy/pasted. Install software Copy and paste the following commands sudo apt-get update && sudo apt-get -y ...Tags: Basic, command-line, run, BLAST, blastn, blastp
2237 days ago
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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...417 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]...2510 days ago
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