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_...2207 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...840 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...2496 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...2318 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...2102 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...1249 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...212 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 -...2615 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...598 days ago
Tags: Blastn, BLAST, Nucleotide, Alignment, Database, NR, Contig, NGS
2839 days ago
RepeatMasker compatible blast tool
RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler. RMBlast supports RepeatMasker searches by adding a...Tags: RMBlast, Repeat, Maskers, Blastn, blast, Download
1939 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...386 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]...2480 days ago