<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/30440?offset=190 https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects Fri, 09 Nov 2018 13:34:56 -0600 https://bioinformaticsonline.com/bookmarks/view/38169/amstat-display-statistics-of-large-sequence-files-from-next-generation-sequencing-projects <![CDATA[AMStat: display statistics of large sequence files from next generation sequencing projects]]> SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

]]> Neel https://bioinformaticsonline.com/videolist/watch/20585/dna-transcription-advanced Thu, 29 Jan 2015 05:31:42 -0600 https://bioinformaticsonline.com/videolist/watch/20585/dna-transcription-advanced <![CDATA[DNA Transcription (Advanced)]]>

Transcription is the process by which the information in DNA is copied into messenger RNA (mRNA) for protein production. Originally created for DNA Interactive ( http://www.dnai.org ). TRANSCRIPT: The Central Dogma of Molecular Biology: "DNA makes RNA makes protein" Here the process begins. Transcription factors assemble at a specific promoter region along the DNA. The length of DNA following the promoter is a gene and it contains the recipe for a protein. A mediator protein complex arrives carrying the enzyme RNA polymerase. It manoeuvres the RNA polymerase into place... inserting it with the help of other factors between the strands of the DNA double helix. The assembled collection of all these factors is referred to as the transcription initiation complex... and now it is ready to be activated. The initiation complex requires contact with activator proteins, which bind to specific sequences of DNA known as enhancer regions. These regions may be thousands of base pairs distant from the start of the gene. Contact between the activator proteins and the initiation-complex releases the copying mechanism. The RNA polymerase unzips a small portion of the DNA helix exposing the bases on each strand. Only one of the strands is copied. It acts as a template for the synthesis of an RNA molecule which is assembled one sub-unit at a time by matching the DNA letter code on the template strand. The sub-units can be seen here entering the enzyme through its intake hole and they are joined together to form the long messenger RNA chain snaking out of the top.

]]> https://bioinformaticsonline.com/researchlabs/view/23209/bisr-jaipur Tue, 07 Jul 2015 23:12:26 -0500 <![CDATA[BISR Jaipur]]> The Bioinformatics Centre at BISR has created an infrastructure for providing facilities to the users working in the field of Biological Sciences. The users of Rajasthan, Jaipur in particular, are using facilities available at the Bioinformatics Centre extensively. The centre has leased line Internet connection as well latest Bioinformatics software for sequence and structure analysis. The centre provides the following services:

Bioinformatics supports to researchers
Customized training in Bioinformatics for researchers and faculty members
Support in Installing, implementing and maintaining software on computer.
Create awareness for taking preventive measure against data security
Organize workshops on thrust ares of Bioinformatics
Research Training to students of Biotechnology and Bioinformatics

More at http://bioinfo.bisr.res.in/index.php

]]> https://bioinformaticsonline.com/researchlabs/view/26828/bioinfolab Fri, 25 Mar 2016 11:05:35 -0500 <![CDATA[BioinfoLab]]> Laboratory of Statistics and Computational tools for Bioinformatics

The Laboratory of Statistics and Computational tools for Bioinformatics (BioinfoLab) is hosted at the Istituto per le Applicazioni del Calcolo "Mauro Picone" - CNR . The laboratory has been officially opened in 2012 with the support of Programma Operativo Nazionale "Ricerca e Competitività" 2007-2013 (PON "R&C"), and it incorporates several expertise and research activities started since 2007, and supported by several CNR projects. Main interest of BioinfoLab is to develop novel statistical methods and computational tools for the analysis of high dimensional data arising from "Multi-omics" applications. In particular, current activities involve the analysis of ChIP-seq and RNA-seq experiments.

More at http://bioinfo.na.iac.cnr.it/BioinfoLab/index.html

]]> https://bioinformaticsonline.com/bookmarks/view/26409/ucsc-genome-browser-and-blat-software Thu, 18 Feb 2016 03:18:57 -0600 https://bioinformaticsonline.com/bookmarks/view/26409/ucsc-genome-browser-and-blat-software <![CDATA[UCSC Genome Browser and Blat software !]]> This directory contains Genome Browser and Blat application binaries built for standalone
command-line use on various supported Linux and UNIX platforms. To determine which set of binaries
to download, type "uname -a" on the command line to display your machine type. In most cases the
usage statement for the application can be viewed by running the binary with no arguments.

The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. A
license is required for commercial download and installation of these binaries, with the exception
of items built from the following source code directories, which are freely available for all uses:

 - kent/src/utils (includes big* tools)
 - kent/src/lib
 - kent/src/hg/autoSql
 - kent/src/hg/autoXml

For information about commercial licensing of the Genome Browser software, see
http://genome.ucsc.edu/license/. The Blat and In-Silico PCR software may be commercially
licensed through Kent Informatics (http://www.kentinformatics.com).

More at http://hgdownload.cse.ucsc.edu/admin/exe/

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/26573/efficient-genome-searching-with-biostrings-and-the-bsgenome-data-package Mon, 07 Mar 2016 05:18:06 -0600 https://bioinformaticsonline.com/bookmarks/view/26573/efficient-genome-searching-with-biostrings-and-the-bsgenome-data-package <![CDATA[Efficient genome searching with Biostrings and the BSgenome data package]]> Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

]]> Aasha https://bioinformaticsonline.com/bookmarks/view/26968/scalce Fri, 15 Apr 2016 05:09:51 -0500 https://bioinformaticsonline.com/bookmarks/view/26968/scalce <![CDATA[SCALCE]]> SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths. 

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

]]> Surabhi Chaudhary https://bioinformaticsonline.com/bookmarks/view/27092/medea-comparative-genomic-visualization-with-adobe-flash Tue, 26 Apr 2016 12:15:16 -0500 https://bioinformaticsonline.com/bookmarks/view/27092/medea-comparative-genomic-visualization-with-adobe-flash <![CDATA[MEDEA: Comparative Genomic Visualization with Adobe Flash]]> As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes Wed, 27 Apr 2016 11:07:59 -0500 https://bioinformaticsonline.com/bookmarks/view/27099/rasttk-algorithm-for-building-custom-annotation-pipelines-and-annotating-batches-of-genomes <![CDATA[RASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes]]> The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

More at http://www.nature.com/articles/srep08365

Address of the bookmark: http://rast.nmpdr.org/

]]> Abhi https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines Sat, 21 May 2016 22:42:16 -0500 https://bioinformaticsonline.com/bookmarks/view/27463/bpipe-a-tool-for-running-and-managing-bioinformatics-pipelines <![CDATA[Bpipe - a tool for running and managing bioinformatics pipelines]]> Bpipe provides a platform for running big bioinformatics jobs that consist of a series of processing stages - known as 'pipelines'.

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

]]> Radha Agarkar