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Results for "FASTA/Q"

Blogs

• • Jit@jit.aber

  

  Computer simulation of genetic mechanism !!

  Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyz...

  3026 days ago

• • Jit@jit.aber

  

  Ancestral sequence reconstruction (ASR) or ancestral gene/sequence reconstruction/resurrection tools to study molecular evolution

  Ancestral sequence reconstruction (ASR) – also known as ancestral gene/sequence reconstruction/resurrection – is a technique used in the stud...

  2581 days ago

• +7 more Blogs

Bookmarks

• • Rahul Agarwal@raag

  

  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...

  3961 days ago

• • Abhimanyu Singh@abhimanyu

  

  Barrnap: Bacterial ribosomal RNA predictor

  Barrnap predicts the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S...

  2601 days ago

• +58 more Bookmarks

Files

• • Jit@jit.aber

  

  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.pl

  3919 days ago

• • Jit@jit.aber

  

  Clean the FASTA file

  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.  

  3917 days ago

• +1 more Files

Pages

• • Jitendra Narayan@admin

  

  Bio++ : C Language libraries for your biological need

  C has always been a language that never attempts to tie a programmer down - it allows for easy implementation, it comes with a genuinely useful standard library that ca...

  3998 days ago

• • Jitendra Narayan@admin

  

  Bioinformatics Articles links

  I found several useful bioinformatics articles which exaplain, define and elaborate the bioinformatics in scientific way. Therefore, instead of writting it again I...

  3972 days ago

• +3 more Pages

Top-level pages

• • Jitendra Narayan@admin

  

  Useful Links for Bioinformaticians

  Bioinformatics demands knowledge of various inter-linked subjects. This page provide links of some the good computer, biology and related tutorials.  Introduction...

  3181 days ago

• • Abhimanyu Singh@abhimanyu

  

  Perl one-liner for bioinformatician !!!

  With the emergence of NGS technologies, and sequencing data most of the bioinformaticians mung and wrangle around massive amounts of genomics text. There are several "s...

  3679 days ago

• +17 more Top-level pages

Wire posts

• • Rahul Nayak@rahul

  

  GenBank to FASTA format conversion, Written By Junguk HUR http://tinyurl.com/ntp7w5v #Perl #FASTA #Genbank

  3919 days ago

• • Jit@jit.aber

  

  perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

  3672 days ago

• +81 more Wire posts

News

• • ArrayGen Technologies@arraygen

  

  ArrayGen Next Generation Genome Browser Coming Soon !!!

  The ANG genome browser is a visualization tool, developed by ArrayGen Technologies. This is a fast and an efficient genome browser, built with Javafx and Java swing. AN...

  3127 days ago

• • Jit@jit.aber

  

  New Layout for BLAST ftp Database Site

  As announced previously, the new default database version for BLAST+ is dbV5.  To complete this transition, the ftp database site will be...

  1617 days ago

Video

• • Robert M Willioms@robert

  

  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=PL76D7EE6A6A8AC1C3

  3570 days ago

Bio-Scripts

• • Surabhi Chaudhary@surabhi

  

  Python script to download covid genome !

  #!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has more (1200?), but they require you to sign up import...

  1187 days ago

• • Neel@neelam

  

  Download genome using NCBI esearch command line !

  #Download using command line "NC_005956.1" / "CP003784.1" esearch -db nucleotide -query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleotide -quer...

  1152 days ago

• +111 more Bio-Scripts

Tags

• • BioJoker@biojoker

  

  SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation

  FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not parti...

  Tags: SeqKit, cross-platform, ultrafast, toolkit, FASTA/Q, manipulation

  1983 days ago

Comments

• • LEGE@lege

  

  Comment on "Short-read assembly using Spades !"

  SPAdes (St. Petersburg genome assembler) is a popular tool for short-read assembly. It can assemble reads generated from Illumina, IonTorrent, PacBi...

  471 days ago

• • BioStar@biostar

  

  Comment on "Basic command-line to run BLAST"

  Following steps need to followed while doing any homology search.  BLAST (Basic Local Alignment Search Tool) is a widely used program for sear...

  474 days ago

• +27 more Comments