Tools to detect synteny blocks regions among multiple genomes
The synteny block (which etymologically means “on the same ribbon”) is a collection of contiguous genes located on the same chromosome. These block regions...2603 days ago
Basic command-line to run BLAST
...sudo apt-get update && sudo apt-get -y install python ncbi-blast+ This updates the software list and installs the Python programming language and NCBI BLAST+. Get Data Grab some dat...2237 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 about it. The tutorial is divided in three main par...3630 days ago
YASS :: genomic similarity search tool
YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuris...2918 days ago
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Genome Assembly Tools and Software - PART2 !!
The genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short...2679 days ago
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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...3124 days ago
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Bioinformatician become producer/director !!!
If a Bioinformatician starts producing Hindi Bollywood movies, names will be like this.... BLAST : Eak khoj Munna Bhai Promoter Gene se Genome tak. Maine BLAST ki...3912 days ago
The Best Bioinformatics / Computational Biology Quotes
Bioinformatician are not anti-social; We are just genome friendly. Bioinformatician would love to change the biological world, but they won't give us the genetic cod...3713 days ago
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Bioinformatics 101 - Running BLAST
How to format the database for BLAST, run the command, view the output file, and use BioPerl and Perl to parse the output. By David Francis, Ohio State University. Deli...3890 days ago
Install BLAST in Ubuntu/Linux and Window !
#On ubuntu sudo apt-get install ncbi-blast+ #Ubuntu Conda installation conda...d ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64...http://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64...1140 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public License. # This script will parse a NCBI blastx output file and...2907 days ago
Tags: BLAST, Standalone, BLAST+, Release, Update
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Blast on Docker, Google Cloud, Amazon Cloud
As announced in a previous post, we offer a Docker version of NCBI BLAST+ that you can use locally or on the Google Cloud where we have pre-loaded BLAST databases. We are happy to announce that the same functionality is now available on the Amazon Cloud. ...Tags: NCBI, BLAST+, Google, BLAST databases, Amazon, Cloud
1389 days ago
Comment on "Basic command-line to run BLAST"
Understanding the parameters https://www.arabidopsis.org/Blast/BLASToptions.jsp391 days ago
Comment on "Tools for RNA classification"
There are several tools available for RNA classification, each with its own strengths and limitations. Here are some commonly used tools: Infer...414 days ago