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Computational Proteomics : Lets remember the basics
...utube.com/watch?v=fLSfgNxoVGk http://www.youtube.com/user/periodicvideos For drug design educational material, software, tools, databses, viewer, file format and many more stuff at...3503 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...3926 days ago
Java and BioJava Tutorial links
BioJava provides analytical and statistical routines, parsers for common file formats and allows the manipulation of sequences and 3D structures. The goal of this bookmark is to provide useful links for bioinformatician. Please add more useful Java and BioJava links here ...3919 days ago
Bioinformatics approach to Boar Taint
...average coverage. Short reads generated from these samples mapped to Sus Scrofa version 10.2 reference assembly using Bowtie2. Alignment file then used for calling SNPs an...3805 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.pl3884 days ago
Bio++ : C Language libraries for your biological need
...evolution Data structure and IO Phylogenetic trees.IO from newick files, with support for multiple e...stuction methods Parsimony (NNI)Distance matrices estimation and I/O to files in Phylip format.Distance me...3964 days ago
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Structure of Binary files used for storing sequencing data-bam and sff
...bioinformatician needs to parse binary files like bam and sff. Advantage of binary files is that they occupy less spa...ho looking for structure of Bam and sff file: Bam: http://samtools.sourc...mats&m=doc&s=format#sff Binary file Editor and Viewer: http://mh...3936 days ago
Useful Publications and Websites for Deep Sequencing Data Analysis
...oinformatics 25(16):2078-9, 2009 PubMedCentral SAM format specification file Efficient storage of high th...nd answers on bioinformatics and computational genomics. Information on file formats used by the Universit...3795 days ago
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Update Genome Workbench 2.7.15 released
...f a user error Graphical Sequence View: PDF export fixed rendering of Markers with commas in the name Text View / Flat File: fixed Mac OS rendering issues Text View / Flat File: performance optimization, ex...3737 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. Delivered live at...3913 days ago
Beginners MYSQL Database Tutorial 1 # Download , Install MYSQL and first SQL query
...arches related to install mysql install mysql macSearches related to install mysql and write query install mysql query browser mysql write query to file how to write delete query in...3664 days ago
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Comment on "A quick guide to Phred scaling"
...ity scores are typically encoded in the quality score field of the FASTQ file format, which is a common for...e call and are typically encoded in the quality score field of the FASTQ file format....431 days ago
Comment on "Short-read assembly using Spades !"
...reads. If the reads are paired-end, they should be provided in separate files for each read. Run SPAd...> Replace read1.fastq and read2.fastq with the names of the input files containing the paired-end re...437 days ago