<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/40204?offset=690 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 Fri, 01 Jul 2016 12:09:59 -0500 https://bioinformaticsonline.com/news/view/28199/genome-workbench-2107 <![CDATA[Genome Workbench 2.10.7]]> Genome Workbench 2.10.7 is here! New features include added support for local custom BLAST databases and improvements to Tree View.

For the full list of features, improvements and fixes, see the release notes:https://ncbi.nlm.nih.gov/tools/gbench/releasenotes

New Features

  • BLAST Tool: added support for local custom BLAST databases
  • Graphical Sequence View: added log scaling option for graph tracks
  • Generic Table View: new tutorial added

Bug Fixes and Improvements

  • Project Tree View: Genomic Collections/Assemblies now show accessions, not just names
  • Tree View: layout updated to better accommodate nodes of different sizes
  • Table Import Dialog (MacOS): fixed issue with table visibility
  • Fixed bug where different molecules IDs in GenBank could resolve to the same sequence
  • Graphical Sequence View: fixed issue where sequence track was not shown for some sequences
  • Graphical Sequence View: fixed protein coloration methods
  • Graphical Sequence View: improved rendering of Markers to better indicate boundaries and produce higher quality PDF images
  • Create Gene Model tool: fixed scenario when gene model tool failed with local sequences
  • Search View: ORF Finder – fixed incorrect protein lengths
  • Fixed bug with not opening project file (.gbp) on a click
  • Fixed issues in GVF import
  • Fixed BLAST Search tool against NCBI databases not working
  • Fixed tblastn (protein BLAST) not working in standalone mode
  • Fixed GTF export failure
]]> Gudiya Pal https://bioinformaticsonline.com/bookmarks/view/28566/emboss-apps Wed, 27 Jul 2016 06:00:41 -0500 https://bioinformaticsonline.com/bookmarks/view/28566/emboss-apps <![CDATA[EMBOSS Apps]]> The programs are listed in alphabetical order, Look at the individual applications or go to the GROUPS page to search by category.

EMBASSY applications are described in separate documentation for each package.

Applications in the current release

Address of the bookmark: http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/31100/vaguevelvet-assembler-graphical-front-end Fri, 24 Feb 2017 08:56:49 -0600 https://bioinformaticsonline.com/bookmarks/view/31100/vaguevelvet-assembler-graphical-front-end <![CDATA[VAGUE:Velvet Assembler Graphical Front End]]> VAGUE is a vague acronym for "Velvet Assembler Graphical Front End", which means it is a GUI for the Velvet de novo assembler. The command line version of Velvet can be complicated for beginners to use, but VAGUE makes it clear and simple

More at http://www.vicbioinformatics.com/software.vague.shtml

Address of the bookmark: http://www.vicbioinformatics.com/software.vague.shtml

]]> Jit https://bioinformaticsonline.com/bookmarks/view/28805/bambus Tue, 16 Aug 2016 08:09:15 -0500 https://bioinformaticsonline.com/bookmarks/view/28805/bambus <![CDATA[Bambus]]>

Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with great flexibility in choosing the scaffolding parameters. In particular, Bambus is able to accept contig linking data other than specified by mate-pairs. Such sources of information include alignment to a reference genome (Bambus can directly use the output of MUMmer), physical mapping data, or information about gene synteny.

Address of the bookmark: https://www.cbcb.umd.edu/software/bambus2

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29276/murasaki Fri, 30 Sep 2016 10:22:30 -0500 https://bioinformaticsonline.com/bookmarks/view/29276/murasaki <![CDATA[Murasaki]]> Murasaki is an anchor alignment program that is

  • exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
  • scalable (Arbitrarily parallelizable across multiple nodes using MPI)
  • memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
  • unlimited by pattern length or selection
  • repeat tolerant

image

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics Tue, 04 Oct 2016 14:50:48 -0500 https://bioinformaticsonline.com/bookmarks/view/29305/miro-mirna-omics <![CDATA[MIRO : miRNA omics]]> The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line Wed, 19 Oct 2016 08:06:24 -0500 https://bioinformaticsonline.com/bookmarks/view/29410/entrez-direct-e-utilities-on-the-unix-command-line <![CDATA[Entrez Direct: E-utilities on the UNIX Command Line]]> Entrez Direct (EDirect) is an advanced method for accessing the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command-line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process.

EDirect also provides an argument-driven function that simplifies the extraction of data from document summaries or other results that are returned in structured XML format. This can eliminate the need for writing custom software to answer ad hoc questions. Queries can move seamlessly between EDirect commands and UNIX utilities or scripts to perform actions that cannot be accomplished entirely within Entrez.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/books/NBK179288/

]]> Anjana https://bioinformaticsonline.com/bookmarks/view/29578/plink2 Thu, 27 Oct 2016 11:24:45 -0500 https://bioinformaticsonline.com/bookmarks/view/29578/plink2 <![CDATA[PLINK2]]> This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others. (What's new?) (Credits.) (Methods paper.)

Address of the bookmark: https://www.cog-genomics.org/plink2/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29656/statistics-and-probability Tue, 08 Nov 2016 07:34:25 -0600 https://bioinformaticsonline.com/bookmarks/view/29656/statistics-and-probability <![CDATA[Statistics and probability]]> Topics

Address of the bookmark: https://www.khanacademy.org/math/statistics-probability

]]> Jit https://bioinformaticsonline.com/bookmarks/view/29693/bioistats-online-course Thu, 10 Nov 2016 04:22:51 -0600 https://bioinformaticsonline.com/bookmarks/view/29693/bioistats-online-course <![CDATA[Bioistats Online course]]> One of our primary focuses will be to develop an understanding of the various ways in which we can assign a probability to some chance event. We'll also learn the fundamental properties of probability, investigate how probability behaves, and learn how to calculate the probability of a new chance event.

This book is handy understanding basic concepts.

Address of the bookmark: https://onlinecourses.science.psu.edu/stat414/node/287

]]> Abhimanyu Singh