Results for "fasta"
Users
Skills: FASTA2639 days ago
Blogs
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...2973 days ago
- ...phylogenetic tree. It is designed for large-scale studies, including simulation of multiple replicates and outputs sequences into NEXUS, MEGA, or FASTA formats. MySSP has a fairly s...
2528 days ago
- +7 more Blogs
Bookmarks
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 ...3908 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...2548 days ago
- +58 more Bookmarks
Files
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.pl3865 days ago
- Mostly FASTA file contain NNN characters, which can be replace by random A T G C character with this perl script. It also print the FASTA sequence name, N's counts, nucleotide count and percentage details at command prompt/standard output.
3864 days ago
- +1 more Files
Pages
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,...3945 days ago
- ...ackgrounds of our students, and the career paths of our graduates. Elementary Sequence Analysis - Database Searching by B. Golding Jan 1996. Fasta, blast, blitz, blaze, flash,...
3919 days ago
- +3 more Pages
Top-level pages
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...3128 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/3626 days ago
- +17 more Top-level pages
Wire posts
News
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...3074 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...1563 days ago
Video
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=PL76D7EE6A6A8AC1C33517 days ago
Bio-Scripts
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...1134 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...1099 days ago
- +110 more Bio-Scripts
Tags
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
868 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
3908 days ago
- +2 more Tags
Comments
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...418 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...421 days ago
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