How do I automate extracting multiple gene sequences from multiple genomes?

omicR for R studio creates fasta files, downloads genomes from NCBI using the refseq number, creates databases to run BLAST+, runs BLAST+ and filters these results to obtain the best match per sequence. These scripts can be used to run BLAST alignment of short-read (DArTseq data) and long-read sequences (Illumina, PacBio… etc). You can use refer…

Automações para realizar alinhamentos em grande escala com o Blast

The impact of transitive annotation on the training of taxonomic classifiers

DNA barcoding analysis pipeline

A typesafe Scala BLAST API

Filter out sequences in FASTQ files that match a reference genome

MIP_ORACLE: Identifies unique target regions with diagnostic significance in pathogens.

The Blastn (Basic Local Alignment Search Tool for Nucleotides) algorithm with Smith-Waterman scoring implemented for FPGAs

This repository conatins bash scripts for performing a blast search using a custom database of BOLA-DRB3 alleles that were sequenced using Sanger sequencing.

BLAST without Sys.Call()

various tools that help with deep sequencing analysis

PhylUp - a python package to automatically generate alignments (or update alignments and phylogenies) using local sequences or a local Genbank database while controlling for the number of sequences per OTU.

BLAST searches in parallel using GNU Parallel

How to automatically download blastn database, run blastn, and extract blastn hit sequences?

Parser of BLAST results

Pipeline to create phage genome synteny graphics from genbank files

Scripts to run benchmarks of BLAST and PLAST on a supercomputer

Map SNP positions to a supplied reference assembly using BLAST. Filter results for best hit. Output in plink format.