2682 days ago
Computer simulation of genetic mechanism !!
...tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied...3015 days ago
2570 days ago
Download mutliple fasta file from NCBI in one GO!!
...then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click giv...\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta where GIs.txt contains ...3950 days ago
Barrnap: Bacterial ribosomal RNA predictor
...genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). It takes FASTA DNA sequence as input, and wr...2590 days ago
Detect the sequence pattern and its location in fasta file with match and mismatches information.
This script is one of my old script to detect some centromeric pattern in chromosomes. User can also control the number of mismatches allowed through command line .. To run: perl centro.pl3908 days ago
3906 days ago
Bio++ : C Language libraries for your biological need
...a given size).Several containers available for inner storage, with several implementations. Support for alignments.Various I/O formats supported: Fasta, Mase, CLustal, Phylip, DCSE,...3988 days ago
3961 days ago
Useful Links for Bioinformaticians
...o analysing sequence databases Sequence Comparison (Keith Robison) Database Research at Penn Biology, E. W. Myers Bill Pearson talks about Fasta Bioinformatics: Elementary S...3170 days ago
Perl one-liner for bioinformatician !!!
...otations/ http://genomics-array.blogspot.com/2010/11/some-unixperl-oneliners-for.html http://bioexpressblog.wordpress.com/2013/04/05/split-multi-fasta-sequence-file/3668 days ago
ArrayGen Next Generation Genome Browser Coming Soon !!!
...nalysis. It is platform independent and much simpler to use. The main features are, it supports many standard file formats such as GFF, BED, GTF, FASTA, VCF, BAM and it can be integ...3116 days ago
New Layout for BLAST ftp Database Site
...v4 subdirectory. As of 1/13/20 the Cloud directory will be frozen with no more new entries. The will be no more updates to dbV4 databases. The FASTA directory will contain nr, nt...1606 days ago
Sequence Viewer: Download Transcripts, Exons and Proteins
How to download FASTA sequence for certain gene features while in the NCBI's Sequence Viewer. Sequence Viewer homepage: www.ncbi.nlm.nih.gov/projects/sviewer/ Sequence Viewer playlist: https://www.youtube.com/playlist?list=PL76D7EE6A6A8AC1C33560 days ago
Python script to download covid genome !
...x['gene-region'] == "complete": nm = x['accession'] print("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().spl...1176 days ago
Download genome using NCBI esearch command line !
...cleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for ali...fastANI -q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequence...1141 days ago
UniqueKmer: Generate unique KMERs for every contig in a FASTA file
Generate unique k-mers for every contig in a FASTA file. Unique k-mer is consisted of k-mer keys (i.e. ATCGATCCTTAAGG) that are only presented in one contig, but not presented in any other contigs (for both forward and reverse strands). This tool accepts the input of a FASTA file consisting of ...Tags: Unique, Kmer, Mers, Contigs, FASTA, Genome
910 days ago
Download mutliple fasta file from NCBI in one GO!!
if you have less time, then use three ways mentioned in bookmark link to extract/download all fasta sequences in single click given that you already have a list of GIs or accession IDs . Alternatively, use one liner perl script: perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if @A...Tags: fasta, multiple fasta, ncbi, entrez, perl
3950 days ago
Comment on "Short-read assembly using Spades !"
...output: Once SPAdes has finished running, check the output directory for the assembled contigs. The contigs will be saved in a file named contigs.fasta. You can view the contigs usi...461 days ago
Comment on "Basic command-line to run BLAST"
...nd tblastx. Choose the program that is appropriate for your query and database. Prepare the query sequence: The query sequence should be in a FASTA format and can be entered dir...463 days ago