<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/26375?offset=50 https://bioinformaticsonline.com/bookmarks/view/42035/pannzer-a-fully-automated-service-for-functional-annotation-of-prokaryotic-and-eukaryotic-proteins-of-unknown-function Thu, 13 Aug 2020 09:57:24 -0500 https://bioinformaticsonline.com/bookmarks/view/42035/pannzer-a-fully-automated-service-for-functional-annotation-of-prokaryotic-and-eukaryotic-proteins-of-unknown-function <![CDATA[PANNZER: a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.]]> PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function.

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE) and GO classes.

PANNZER2 processes bacterial proteomes in minutes and eukaryotic proteomes in an hour. You can use AAI-profiler to summarize a proteome's species neighbors and reveal taxonomic identity or contamination.

Address of the bookmark: http://ekhidna2.biocenter.helsinki.fi/sanspanz/#

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/31552/multigenome-assembly Tue, 14 Mar 2017 04:41:23 -0500 https://bioinformaticsonline.com/bookmarks/view/31552/multigenome-assembly <![CDATA[Multigenome assembly]]> This project contains scripts and tutorials on how to assemble individual microbial genomes from metagenomes, as described in:

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen, Philip Hugenholtz, Adam Skarshewski, Gene W. Tyson, Kåre L. Nielsen and Per .H. Nielsen

Nature Biotechnology 2013, doi: 10.1038/nbt.2579

See the associated online guide for detailed information.

https://github.com/MadsAlbertsen/multi-metagenome

Address of the bookmark: https://github.com/MadsAlbertsen/multi-metagenome

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r Fri, 13 Aug 2021 07:44:05 -0500 https://bioinformaticsonline.com/bookmarks/view/43254/quasr-quantification-and-annotation-of-short-reads-in-r <![CDATA[QuasR: Quantification and annotation of short reads in R]]> The QuasR package (short for Quantify and annotate short reads in R) integrates the functionality of several R packages (such as IRanges (Lawrence et al. 2013) and Rsamtools) and external software (e.g. bowtie, through the Rbowtie package, and HISAT2, through the Rhisat2 package). The package aims to cover the whole analysis workflow of typical high throughput sequencing experiments, starting from the raw sequence reads, over pre-processing and alignment, up to quantification. A single R script can contain all steps of a complete analysis, making it simple to document, reproduce or share the workflow containing all relevant details.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/QuasR/inst/doc/QuasR.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/31714/krona Wed, 22 Mar 2017 04:47:35 -0500 https://bioinformaticsonline.com/bookmarks/view/31714/krona <![CDATA[Krona]]> Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats. The interactive charts are self-contained and can be viewed with any modern web browser (see Browser support).

image

Address of the bookmark: https://github.com/marbl/Krona/wiki

]]> Jit https://bioinformaticsonline.com/bookmarks/view/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation Mon, 29 May 2017 05:39:29 -0500 https://bioinformaticsonline.com/bookmarks/view/33219/dbcan-a-web-server-and-database-for-automated-carbohydrate-active-enzyme-annotation <![CDATA[dbCAN: a web server and DataBase for automated Carbohydrate-active enzyme ANnotation]]> dbCAN is a web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE. Similar resources on the web include CAZy database and CAT. All data in dbCAN are generated based on the family classification from CAZy database while it has the following unique features compared with CAZy database and CAT:

  • dbCAN provides the capability of automated and comprehensive CAZyme annotation of a given genome submitted by the user;
  • dbCAN provides an explicitly defined signature domain for each and every CAZyme family along with its location in all the relevant full-length CAZyme proteins in all sequenced genomes;
  • dbCAN provides the most complete set of metagenomic CAZyme genes published so far and represents the first step towards discovering novel CAZyme catalysts in metagenomes;
  • dbCAN provides a subfamily classification of the existing CAZyme families based on sequence similarities;
  • dbCAN make all pre-computed data freely available to the public, including sequence alignments, hidden markov models (HMMs) and phylogenies of the signature domain regions in each and every CAZyme family and subfamily.

dbCAN is updated regularly when CAZy database created new families based on latest literature.

Address of the bookmark: http://csbl.bmb.uga.edu/dbCAN/index.php

]]> Jit https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes Sun, 02 Apr 2017 15:53:47 -0500 https://bioinformaticsonline.com/bookmarks/view/32018/tmap-torrent-mapping-alignment-program-general-notes <![CDATA[TMAP - torrent mapping alignment program General Notes]]> TMAP - torrent mapping alignment program General Notes

TMAP is a fast and accurate alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.

  • The latest TMAP is unsupported. To use a supported version, please see the TMAP version associated with a Torrent Suite release below.

  • Get the latest source code:

    git clone git://github.com/iontorrent/TMAP.git
 cd TMAP
 git submodule init
 git submodule update

https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

Address of the bookmark: https://github.com/iontorrent/TS/tree/master/Analysis/TMAP

]]> Poonam Mahapatra https://bioinformaticsonline.com/view/459 Thu, 11 Jul 2013 14:39:19 -0500 https://bioinformaticsonline.com/view/459 <![CDATA[Python vs Perl]]> Why bioinformatician still using Perl when Python is easy to code, good in ReXp and faster than perl?

]]> Rahul Agarwal https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 Mon, 10 Apr 2017 04:45:40 -0500 https://bioinformaticsonline.com/bookmarks/view/32131/wgs-celera-assembler-version-83rc2 <![CDATA[WGS Celera Assembler version 8.3rc2]]> These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.

This distribution package provides a stable, tested, documented version of the software.  The distribution is usable on most Unix-like platforms, and some platforms have pre-compiled binary distributions ready for installation.

The source code package includes full source code (revision 4627), Makefiles, and scripts.  A subset of the kmer package (http://kmer.sourceforge.net/, version r1994), used by some modules of Celera Assembler, is included.  This distribution includes [http://samtools.sourceforge.net/ SAMtools], [http://www.cbcb.umd.edu/software/jellyfish/ Jellyfish 2.0], [https://github.com/pbjd/pbutgcns PBUTGCNS], [https://github.com/PacificBiosciences/pbdagcon PBDAGCON], [https://github.com/PacificBiosciences/BLASR BLASR], and parts of the [https://github.com/PacificBiosciences/FALCON/tree/v0.1.3 Falcon assembler].

Full documentation can be found online at http://wgs-assembler.sourceforge.net/.

Interesting scripts within it

urbe@urbo214b[bin] ls                                                        []
-rwxrwxr-x 1 urbe urbe  11K Apr 10 11:41 addCNSToStore
-rwxrwxr-x 1 urbe urbe 575K Apr 10 11:41 addReadsToUnitigs
-rwxrwxr-x 1 urbe urbe 128K Apr 10 11:41 analyzeBest
-rwxrwxr-x 1 urbe urbe 257K Apr 10 11:41 analyzePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 analyzeScaffolds
-rwxrwxr-x 1 urbe urbe 224K Apr 10 11:41 asmOutputFasta
-rwxrwxr-x 1 urbe urbe 448K Apr 10 11:41 asmOutputStatistics
-rwxrwxr-x 1 urbe urbe 2,4K Apr 10 11:41 asmToAGP.pl
-rwxrwxr-x 1 urbe urbe 7,6M Apr 10 11:41 blasr
-rwxrwxr-x 1 urbe urbe 1,6M Apr 10 11:41 bogart
-rwxrwxr-x 1 urbe urbe 183K Apr 10 11:41 bogus
-rwxrwxr-x 1 urbe urbe 272K Apr 10 11:41 bogusness
-rwxrwxr-x 1 urbe urbe 247K Apr 10 11:41 buildPosMap
-rwxrwxr-x 1 urbe urbe 213K Apr 10 11:41 buildRefContigs
-rwxrwxr-x 1 urbe urbe 990K Apr 10 11:41 buildUnitigs
-rwxrwxr-x 1 urbe urbe  18K Apr 10 11:41 ca2ace.pl
-rwxrwxr-x 1 urbe urbe  12K Apr 10 11:41 caqc_help.ini
-rwxrwxr-x 1 urbe urbe  61K Apr 10 11:41 caqc.pl
-rwxrwxr-x 1 urbe urbe  23K Apr 10 11:41 cat-corrects
-rwxrwxr-x 1 urbe urbe  24K Apr 10 11:41 cat-erates
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 cgw
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 cgwDump
-rwxrwxr-x 1 urbe urbe 204K Apr 10 11:41 chimChe
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 chimera
-rwxrwxr-x 1 urbe urbe 220K Apr 10 11:41 classifyMates
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:41 classifyMatesApply
-rwxrwxr-x 1 urbe urbe 215K Apr 10 11:41 classifyMatesPairwise
-rwxrwxr-x 1 urbe urbe 366K Apr 10 11:41 computeCoverageStat
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 convert-fasta-to-v2.pl
-rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 convertOverlap
-rwxrwxr-x 1 urbe urbe 119K Apr 10 11:41 convertSamToCA
-rwxrwxr-x 1 urbe urbe  20K Apr 10 11:41 convertToPBCNS
-rwxrwxr-x 1 urbe urbe 197K Apr 10 11:41 correct-frags
-rwxrwxr-x 1 urbe urbe 259K Apr 10 11:41 correct-olaps
-rwxrwxr-x 1 urbe urbe 520K Apr 10 11:41 correctPacBio
-rwxrwxr-x 1 urbe urbe 540K Apr 10 11:41 ctgcns
-rwxrwxr-x 1 urbe urbe 162K Apr 10 11:40 deduplicate
-rwxrwxr-x 1 urbe urbe  37K Apr 10 11:41 demotePosMap
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 dumpCloneMiddles
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:41 dumpPBRLayoutStore
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 dumpSingletons
-rwxrwxr-x 1 urbe urbe 171K Apr 10 11:41 erate-estimate
-rwxrwxr-x 1 urbe urbe 221K Apr 10 11:40 estimate-mer-threshold
-rwxrwxr-x 1 urbe urbe 1,5M Apr 10 11:41 extendClearRanges
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 extendClearRangesPartition
-rwxrwxr-x 1 urbe urbe 205K Apr 10 11:40 extractmessages
-rwxrwxr-x 1 urbe urbe 7,2M Apr 10 11:41 falcon_sense
-rwxrwxr-x 1 urbe urbe 9,8K Apr 10 11:41 fastaToCA
-rwxrwxr-x 1 urbe urbe 124K Apr 10 11:40 fastqAnalyze
-rwxrwxr-x 1 urbe urbe 137K Apr 10 11:40 fastqSample
-rwxrwxr-x 1 urbe urbe  62K Apr 10 11:40 fastqSimulate
-rwxrwxr-x 1 urbe urbe 121K Apr 10 11:40 fastqSimulate-sort
-rwxrwxr-x 1 urbe urbe 246K Apr 10 11:40 fastqToCA
-rwxrwxr-x 1 urbe urbe 140K Apr 10 11:41 filterOverlap
-rwxrwxr-x 1 urbe urbe 341K Apr 10 11:40 finalTrim
-rwxrwxr-x 1 urbe urbe 228K Apr 10 11:41 fixUnitigs
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 fragmentDepth
-rwxrwxr-x 1 urbe urbe  29K Apr 10 11:41 fragsInVars
-rwxrwxr-x 1 urbe urbe 545K Apr 10 11:41 frgs2clones
-rwxrwxr-x 1 urbe urbe 398K Apr 10 11:40 gatekeeper
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:40 gatekeeperbench
-rwxrwxr-x 1 urbe urbe 167K Apr 10 11:40 gkpStoreCreate
-rwxrwxr-x 1 urbe urbe 147K Apr 10 11:40 gkpStoreDumpFASTQ
-rwxrwxr-x 1 urbe urbe 184K Apr 10 11:41 greedyFragmentTiling
-rwxrwxr-x 1 urbe urbe 1,6K Apr 10 11:41 greedy_layout_to_IUM
-rwxrwxr-x 1 urbe urbe 142K Apr 10 11:40 initialTrim
-rwxrwxr-x 1 urbe urbe 967K Apr 10 11:41 jellyfish
-rwxrwxr-x 1 urbe urbe 219K Apr 10 11:41 markRepeatUnique
-rwxrwxr-x 1 urbe urbe 273K Apr 10 11:40 markUniqueUnique
-rwxrwxr-x 1 urbe urbe 114K Apr 10 11:40 mercy
-rwxrwxr-x 1 urbe urbe 3,8K Apr 10 11:41 mergeqc.pl
-rwxrwxr-x 1 urbe urbe 422K Apr 10 11:40 merTrim
-rwxrwxr-x 1 urbe urbe 125K Apr 10 11:40 merTrimApply
-rwxrwxr-x 1 urbe urbe 376K Apr 10 11:40 meryl
-rwxrwxr-x 1 urbe urbe 176K Apr 10 11:41 metagenomics_ovl_analyses
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:41 olap-from-seeds
-rwxrwxr-x 1 urbe urbe 275K Apr 10 11:41 outputLayout
-rwxrwxr-x 1 urbe urbe 229K Apr 10 11:41 overlapInCore
-rwxrwxr-x 1 urbe urbe 144K Apr 10 11:40 overlap_partition
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStats
-rwxrwxr-x 1 urbe urbe 179K Apr 10 11:41 overlapStore
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:41 overlapStoreBucketizer
-rwxrwxr-x 1 urbe urbe 175K Apr 10 11:41 overlapStoreBuild
-rwxrwxr-x 1 urbe urbe  33K Apr 10 11:41 overlapStoreIndexer
-rwxrwxr-x 1 urbe urbe  48K Apr 10 11:41 overlapStoreSorter
-rwxrwxr-x 1 urbe urbe 604K Apr 10 11:40 overmerry
lrwxrwxrwx 1 urbe urbe    4 Apr 10 11:41 pacBioToCA -> PBcR
-rwxrwxr-x 1 urbe urbe 131K Apr 10 11:41 PBcR
-rwxrwxr-x 1 urbe urbe 2,9M Apr 10 11:41 pbdagcon
-rwxrwxr-x 1 urbe urbe 1,9M Apr 10 11:41 pbutgcns
-rwxrwxr-x 1 urbe urbe 201K Apr 10 11:40 remove_fragment
-rwxrwxr-x 1 urbe urbe 153K Apr 10 11:40 removeMateOverlap
-rwxrwxr-x 1 urbe urbe 2,5K Apr 10 11:41 replaceUIDwithName-fastq
-rwxrwxr-x 1 urbe urbe 1,2K Apr 10 11:41 replaceUIDwithName-posmap
-rwxrwxr-x 1 urbe urbe 1,3M Apr 10 11:41 resolveSurrogates
-rwxrwxr-x 1 urbe urbe 139K Apr 10 11:41 rewriteCache
-rwxrwxr-x 1 urbe urbe 232K Apr 10 11:41 runCA
-rwxrwxr-x 1 urbe urbe  88K Apr 10 11:41 runCA-dedupe
-rwxrwxr-x 1 urbe urbe  14K Apr 10 11:41 runCA-overlapStoreBuild
-rwxrwxr-x 1 urbe urbe 3,6K Apr 10 11:41 run_greedy.csh
-rwxrwxr-x 1 urbe urbe 297K Apr 10 11:40 sffToCA
-rwxrwxr-x 1 urbe urbe  13K Apr 10 11:40 show-corrects
-rwxrwxr-x 1 urbe urbe 557K Apr 10 11:41 splitUnitigs
-rwxrwxr-x 1 urbe urbe 1,4M Apr 10 11:41 terminator
drwxrwxr-x 2 urbe urbe 4,0K Apr 10 11:41 TIGR
-rwxrwxr-x 1 urbe urbe 526K Apr 10 11:41 tigStore
-rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracearchiveToCA
-rwxrwxr-x 1 urbe urbe  35K Apr 10 11:41 tracedb-to-frg.pl
-rwxrwxr-x 1 urbe urbe  44K Apr 10 11:41 trimFastqByQVWindow
-rwxrwxr-x 1 urbe urbe  18K Apr 10 11:40 uidclient
-rwxrwxr-x 1 urbe urbe 589K Apr 10 11:41 unitigger
-rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v8-to-v9
-rwxrwxr-x 1 urbe urbe  42K Apr 10 11:40 upgrade-v9-to-v10
-rwxrwxr-x 1 urbe urbe  854 Apr 10 11:41 utg2fasta
-rwxrwxr-x 1 urbe urbe 731K Apr 10 11:41 utgcns
-rwxrwxr-x 1 urbe urbe 561K Apr 10 11:41 utgcnsfix


Address of the bookmark: http://wgs-assembler.sourceforge.net/wiki/index.php/Main_Page

]]> Jit https://bioinformaticsonline.com/opportunity/view/840/junior-research-fellow-jrf Sat, 13 Jul 2013 11:17:22 -0500 <![CDATA[Junior Research Fellow (JRF)]]> School of Biotechnology
Gautam Buddha University
Greater Noida, UP - 201310

Applications are invited for one position of Junior Research Fellow (JRF) in a Department of Biotechnology (DBT) sponsored research project entitled “Design, synthesis and evaluation of potent aminopeptidase inhibitors for malarial therapy” under the supervision of Dr. Shakti Sahi.

The monthly fellowship of JRF will be Rs 12,000/- plus HRA as per the University rules.

Essential Qualification: Master degree in any discipline of Life Science with NET qualified.

Desirable Qualification: Preference will be given to candidates having research experience in in silico drug designing/Bioinformatics.

Interested candidates may send their resume to undersigned on or before 14th July 2013 by post-mail/e-mail shaktis@gbu.ac.in or shaktisahi@gmail.com. No TA and DA will be paid for appearing for the interview. Dr. Shakti Sahi (Principle Investigator)

Advertisement:
www.gbu.ac.in/Recruitment/JRF_Advt_DBTProject_Shakt

]]> https://bioinformaticsonline.com/bookmarks/view/32184/metagenomics-assembly-workshop Tue, 18 Apr 2017 04:28:19 -0500 https://bioinformaticsonline.com/bookmarks/view/32184/metagenomics-assembly-workshop <![CDATA[Metagenomics assembly workshop !!]]>
Next 

 

Address of the bookmark: http://denbi-metagenomics-workshop.readthedocs.io/en/latest/index.html

]]> Jit