Results for "multiple fasta"
Blogs
In comparative genome analysis work, we usually compare more than two genomes and looks for syntenic regions amongs...ect designed to provide a visual means for simultaneously comparing genomes of multi...3934 days ago
Tools to detect synteny blocks regions among multiple genomes
The synteny block (which etymologically means “on the same ribbon&rdq...regardless of whether it encompasses multiple genes, an area containing sin...for finding regions syntenic across multiple genomes and measuring the ext...ze and interrogate comparisons among multi...2605 days ago
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Bookmarks
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 giv...print:chomp;$i{$_}=1 if @ARGV' GIs.txt >sequence.fasta where GIs.txt contains ...3905 days ago
A Brief Bioinformatics Tutorial
This is about how to use a computer to find what is known about a gene of interest and also how to get new insights a...st it against the database of your choice to find homologues, how to perform a multi...3631 days ago
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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.pl3862 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.
3861 days ago
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Pages
Bio++ : C Language libraries for your biological need
...implementations. Support for alignments.Various I/O formats supported: Fasta, Mase, CLustal, Phylip, DCSE, Ge...ture and IO Phylogenetic trees.IO from newick files, with support for multiple entries. Phylogenetic rec...3942 days ago
- Ruby was created by Yukihiro Matsumoto, who wished to create a new language that balanced functional programming with...was influenced primarily by Perl, Smalltalk, Eiffel, and Lisp. Ruby supports multi...
3942 days ago
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Top-level pages
- ...; cannot take into account proteins that have multiple functions depending on contex...nservation patters at all sequence positions. Multiple sequence alignments are usefu...exible sequence similarity searching with the FASTA3 program package. Methods Mol...
3942 days ago
- An algorithm is a computable set of steps to achieve a desired result. We use algorithms every day. For example, a r...e/~amclysag/nwswat.html•http://laguerre.psc.edu/biomed/TUTORIALS/SEQUENCE/MULTI...
3941 days ago
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Wire posts
News
- PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to...lutionary history of genes through the visualization of phylogenetic trees and multi...
3913 days ago
Atlas of ancient inter-ethnic group !!!
Now a dayz, almost 3% of the world's population lived outside their country of origin. These migration is...curred between genetically similar groups, and scenarios involving multiple waves of mixing over time or between multi...3727 days ago
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Opportunity posts
Structural polymorphism analysis from NGS data
The LabEx BASC (Biodiversity, Agroecosystems, Society, Climate), a network of 13 laboratories of the Paris-Saclay Sci...detection of polymorphisms including structural variants, of the comparison of multi...3943 days ago
- van Noort Group is looking for PhD fellows We currently access an unprecedented knowledge on the basic components...e being developed with the capacity to systematically measure the behaviour of multi...
3943 days ago
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ResearchLabs posts
- Raphael Lab research is focused on Bioinformatics and Computational Biology. Current research interests include ne...mutations in cancer. Earlier research included topics in comparative genomics, multi...
3222 days ago
- Focusing on understanding the molecular mechanisms that regulate mRNA translation, localization and stability and rol...y regulate expression of more than a half of eukaryotic genes, thus, affecting multi...
3031 days ago
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Video
Computer Theory & Genetics: George Chao at TEDxUMNSalon
George Chao is an undergraduate senior studying Genetics and Computer Science at the University of Minnesota. Having...research as soon as he entered the university, he has worked in labs spanning multi...3910 days ago
Introduction to Bioinformatics - Week 8 - Lecture 1
Middle East Technical University OpenCourseWare [ http://ocw.metu.edu.tr ] Course Title: Introduction to Bioinformatics Lecture Title: Multiple Sequence Alignment Algorithms Instructor: Assoc. Prof. Tolga CAN For Lecture Notes: http://ocw.metu.edu.tr/course/view.php?id=373891 days ago
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Bio-Scripts
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # ht...("downloading", nm) dna = Entrez.efetch(db='nucleotide',id=nm, rettype = 'fasta', retmode= 'text').read().spl...1131 days ago
Download genome using NCBI esearch command line !
#Download using command line "NC_005956.1" /...-query "NC_005956.1" | efetch -format fasta > seq1.fa esearch -db nucleo...-query "CP003784.1" | efetch -format fasta > seq2.fa #fastANI for ali...-q seq1.fa -r seq2.fa --visualize -o fastani.out #Plot using sequence...1096 days ago
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Groups
Our research interest falls in the broad field of bioinformatics and, more specifically into Computational Systems an...ental and pathological processes relevant to human health. We collaborate with multi...3938 days ago
Metabolomics is the comprehensive and quantitative analysis of multiple metabolites in biological samples. Metabolome is the complete set of small-molecule metabolites found within a...3700 days ago
Tags
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
3905 days ago
Comments
- ...ommand line options. $ ./fastANI -h One to One. Compu...le reference genome: $ ./fastANI -q [QUERY_GENOME] -r [REFERENC...to Many. When there are multiple query genomes and multiple reference genomes: $ ./fastANI --ql [QUERY_LIST] --rl [REF...
1096 days ago
Comment on "Sibelia: A comparative genomics tool"
...Sibelia -s loose <input FASTA file(s)> For example:...-s loose Helicobacter_pylori.fasta Important note -- "Sibelia" r...equence: 1. Header line -- FASTA header of the sequence (start...lia" performs computations in multiple stages. Every stage produc...1279 days ago
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