BOL: Related items

BRAKER: pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes

Jit — Thu, 01 Sep 2016 08:02:59 -0500

Gene finding in eukaryotic genomes is notoriously difficult to automate. The task is to design a work flow with a minimal set of tools that would reach state-of-the-art performance across a wide range of species. GeneMark-ET is a gene prediction tool that incorporates RNA-Seq data into unsupervised training and subsequently generates ab initio gene predictions. AUGUSTUS is a gene finder that usually requires supervised training and uses information from RNA-Seq reads in the prediction step. Complementary strengths of GeneMark-ET and AUGUSTUS provided motivation for designing a new combined tool for automatic gene prediction.

http://www.ncbi.nlm.nih.gov/pubmed/26559507

Address of the bookmark: http://bioinf.uni-greifswald.de/bioinf/braker/

DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication

Jit — Tue, 14 Nov 2017 10:26:16 -0600

We developed a prokaryotic genome annotation pipeline, DFAST, that also supports genome submission to public sequence databases. DFAST was originally started as an on-line annotation server, and to date, over 7,000 jobs have been processed since its first launch in 2016. Here, we present a newly implemented background annotation engine for DFAST, which is also available as a standalone command-line program. The new engine can annotate a typical-sized bacterial genome within 10 minutes, with rich information such as pseudogenes, translation exceptions, and orthologous gene assignment between given reference genomes. In addition, the modular framework of DFAST allows users to customize the annotation workflow easily and will also facilitate extensions for new functions and incorporation of new tools in the future.

Availability and Implementation

The software is implemented in Python 3 and runs in both Python 2.7 and 3.4– on Macintosh and Linux systems. It is freely available at https://github.com/nigyta/dfast_core/ under the GPLv3 license with external binaries bundled in the software distribution. An on-line version is also available at https://dfast.nig.ac.jp/.

Address of the bookmark: https://dfast.nig.ac.jp/

JBrowse: Embeddable genome browser built completely with JavaScript and HTML5

Jit — Fri, 29 Jun 2018 09:19:56 -0500

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl. Headline Features: Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed. Scales easily to multi-gigabase genomes and deep-coverage sequencing. Quickly open and view data files on your computer without uploading them to any server. Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with either .tbi or .idx index), REST, and more. BAM, BigBed, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed. Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks. Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance. Can run as a stand-alone app on OSX and Windows using the Electron platform Highly extensible plugin architecture, with a large plugin registry of existing examples here https://gmod.github.io/jbrowse-registry https://jbrowse.org/

Address of the bookmark: https://github.com/GMOD/jbrowse

AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome

Jit — Mon, 23 Dec 2019 10:20:13 -0600

We propose AirLift, a methodology and tool for comprehensively moving mappings and annotations from one genome to another similar genome while maintaining the accuracy of a full mapper.

Address of the bookmark: https://github.com/CMU-SAFARI/AirLift

BLAST nr version 5 database, (nr_v5)

Jit — Fri, 23 Aug 2019 11:35:35 -0500

NCBI have made changes the nr version 5 database, (nr_v5), to facilitate better search results and improved performance by reducing the number of redundant titles in the nr_v5 database used by webBLAST, which is also available for BLAST+ users.

The changes in nr preserve the taxonomic diversity of the entries in the database while reducing the number of titles for identical sequences. GenPept accessions are still accessible via www.ncbi.nlm.nih.gov/protein/$GENBANK_ACCESSION or the IPG website https://www.ncbi.nlm.nih.gov/ipg/.

The "Identical Proteins" link in the alignments section of the webBLAST results takes you to a full list of all accessions associated with a sequence.

For BLAST+ users downloading nr_v5: the database is now approximately 50% smaller, resulting in faster downloads and BLAST searches, and smaller disk space requirements. The database is downloadable at: ftp://ftp.ncbi.nlm.nih.gov/blast/db/v5/

For BLAST+ there is a cleanup script to help you manage the transition to this smaller database. The script removes unused database volumes: ftp://ftp.ncbi.nlm.nih.gov/blast/temp/cleanup-blastdb-volumes.py

Here are the new rules on how we keep titles in nr_v5:

1. We keep all refseq, swissprot, pir and PDB titles.

2. We keep any GenPept titles with a TAXID that has not already been seen in the record.

3. We keep at least five GenPept titles regardless of whether the TAXIDS have been seen before or not in this record.

DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes

Rahul Nayak — Tue, 30 Mar 2021 11:47:28 -0500

Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a key role in the emerging field, synthetic biology.

DEG is freely available at the website http://tubic.tju.edu.cn/deg or http://www.essentialgene.org.

Address of the bookmark: http://www.essentialgene.org/

Download blasr 1.3 version

Jit — Fri, 15 Jun 2018 03:01:20 -0500

DOWNLOAD LINK: https://github.com/BioInf-Wuerzburg/proovread/raw/master/util/blasr-1.3.1/blasr

I'm running "OPERA-LG_v2.0.5/bin/preprocess_reads.pl" and have the following error:

fail to open file './temporarySam'

[bwa_aln_core] write to the disk... 0.09 sec
[bwa_aln_core] 70778880 sequences have been processed.
[bwa_aln_core] calculate SA coordinate... 161.35 sec
[bwa_aln_core] write to the disk... 0.06 sec
[bwa_aln_core] 70989574 sequences have been processed.
[main] Version: 0.7.15-r1140
[main] CMD: bwa aln -t 30 all_p_ctg.fa -
[main] Real time: 2402.523 sec; CPU: 53429.488 sec
[E::hts_open_format] Failed to open file temporarySam
samtools sort: can't open "temporarySam": No such file or directory
[bwa_aln_core] convert to sequence coordinate... 1.00 sec
[bwa_aln_core] refine gapped alignments... 6.07 sec
[bwa_aln_core] print alignments... PREPROCESS:
Fastq format is recognized
[Thu Jun 14 18:16:47 2018] Building bwa index...
bwa index -p all_p_ctg.fa /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa
[Thu Jun 14 18:18:35 2018] Finding the SA coordinates of the reads using BWA aln...
[Thu Jun 14 18:58:37 2018] Generate alignments of reads using bwa sampe...
bwa samse -n 1 all_p_ctg.fa read.sai - | grep '$^@\|XT:A:U$' | /usr/local/bin/samtools view -S -h -b -F 0x4 - | /usr/local/bin/samtools sort -@ 20 -no - temporarySam > FALCON-Unzip-Scaff.bam
Mapping long-reads using blasr...
/home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr -nproc 40 -m 1 -minMatch 5 -bestn 10 -noSplitSubreads -advanceExactMatches 1 -nCandidates 1 -maxAnchorsPerPosition 1 -sdpTupleSize 7 /media/urbe/MyDDrive/ONTdata/allONT/allONT.fasta /home/urbe/Tools/OPERA-LG_v2.0.6/all_p_ctg.fa | cut -d ' ' -f1-5,7-12 | sed 's/ /\t/g' > FALCON-Unzip-Scaff.map
sh: 1: /home/urbe/Tools/SSpace/SSPACE-LongRead_v1-1/blasr: Permission denied
Sorting mapping results...
sort -k1,1 -k9,9g FALCON-Unzip-Scaff.map > FALCON-Unzip-Scaff.map.sort
Analyzing sorted results...
Extracting linking information...
i3 2000 5000
i2 1000 2000
i4 5000 15000
i0 -200 300
i5 15000 40000
i1 300 1000
Repeat detection...
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl pairedEdges_i0 contig_length.dat 100 2
Illegal division by zero at /home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_conflicting_edge.pl line 93.
readline() on closed filehandle FILE at bin/OPERA-long-read.pl line 250.
rm anchor_contig_info.dat contig_length.dat filtered_edges.dat filtered_edges_cov.dat *.sai
rm: cannot remove 'anchor_contig_info.dat': No such file or directory
mv FALCON-Unzip-Scaff.bam FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin//filter_repeat.pl FALCON-Unzip-Scaff-with-repeat.bam repeat.dat | /usr/local/bin/samtools view - -h -S -b > FALCON-Unzip-Scaff.bam
rm FALCON-Unzip-Scaff-with-repeat.bam
/home/urbe/Tools/OPERA-LG_v2.0.6/bin/OPERA-LG config > log
Analyzing 1 library: FALCON-Unzip-Scaff.bam
min library mean : 0
minimum contig length is 500
Current library: 1 out of 7
Analyzing file: pairedEdges_no_repeat_i0
Analyzing file: pairedEdges_no_repeat_i1
Analyzing file: pairedEdges_no_repeat_i2
Analyzing file: pairedEdges_no_repeat_i3
Analyzing file: pairedEdges_no_repeat_i4
Analyzing file: pairedEdges_no_repeat_i5
ln -s results/scaffoldSeq.fasta scaffoldSeq.fasta

To resolve this, try downloading blasr version 1.3 above and re-run :)

Tools for bacterial whole genome annotation

Radha Agarkar — Sat, 16 Dec 2017 17:37:47 -0600

RAST – Web tool (upload contigs), uses the subsystems in the SEED database and provides detailed annotation and pathway analysis. Takes several hours per genome but I think this is the best way to get a high quality annotation (if you have only a few genomes to annotate).

Prokka – Standalone command line tool, takes just a few minutes per genome. This is the best way to get good quality annotation in a flash, which is particularly useful if you have loads of genomes or need to annotate a pangenome or metagenome. Note however that the quality of functional information is not as good as RAST, and you will need several extra steps if you want to do functional profiling and pathway analysis of your genome(s)… which is in-built in RAST.

NCBI Prokaryotic Genome Annotation Pipeline is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).

Genome annotation is a multi-level process that includes prediction of protein-coding genes, as well as other functional genome units such as structural RNAs, tRNAs, small RNAs, pseudogenes, control regions, direct and inverted repeats, insertion sequences, transposons and other mobile elements.

PGAP: NCBI has developed an automatic prokaryotic genome annotation pipeline that combines ab initio gene prediction algorithms with homology based methods. The first version of NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP; see Pubmed Article) developed in 2005 has been replaced with an upgraded version that is capable of processing a larger data volume. NCBI's annotation pipeline depends on several internal databases and is not currently available for download or use outside of the NCBI environment.

BEACON (automated tool for Bacterial GEnome Annotation ComparisON), a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/.

BlastKOLA: Assigns K numbers to the user's sequence data by BLAST searches, respectively, against a nonredundant set of KEGG GENES. KOALA (KEGG Orthology And Links Annotation) is KEGG's internal annotation tool for K number assignment of KEGG GENES using SSEARCH computation. Annotate Sequence in KEGG Mapper and Pathogen Checker in KEGG Pathogen are special interfaces to this server and can be executed in an interactive mode. BlastKOALA is suitable for annotating fully sequenced genomes.

PAGIT: Provides a toolkit for improving the quality of genome assemblies created via an assembly software. PAGIT compiled four tools: (i) ABACAS which classifies and orientates contigs and estimates the sizes of gaps between them; (ii) IMAGE uses paired-end reads to extend contigs and close gaps within the scaffolds; (iii) ICORN for identifying and correcting small errors in consensus sequences and; (iv) RATT for help annotation. The software was mainly created to analyze parasite genomes of up to about 300 Mb.

MAKER: A portable and easily configurable genome annotation pipeline. MAKER allows smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. It identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER's inputs are minimal and its ouputs can be directly loaded into a Generic Model Organism Database (GMOD). They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER is available for download and can be tested online via the MAKER Web Annotation Service (MWAS).

MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014

Tue, 27 Aug 2013 10:37:08 -0500

RGCB is organizing the 33rd Annual Convention of Indian Association for Cancer Research from 13th to 15th February 2014 with the theme "Discovery, Innovation and Translation in Cancer Research"

Kindly log on to conference website http://rgcb.res.in/IACR2014 for further details and timely updates and registration. We shall truly appreciate if the same be circulated among your friends, scholars and students encouraging them to participate in the meet.

http://210.212.237.38/iacrconference/

GeneBreak: a tool to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach

Jit — Sat, 01 Oct 2016 15:15:29 -0500

Development of cancer is driven by somatic alterations, including numerical and structural chromosomal aberrations. Currently, several computational methods are available and are widely applied to detect numerical copy number aberrations (CNAs) of chromosomal segments in tumor genomes. However, there is lack of computational methods that systematically detect structural chromosomal aberrations by virtue of the genomic location of CNA-associated chromosomal breaks and identify genes that appear non-randomly affected by chromosomal breakpoints across (large) series of tumor samples. ‘GeneBreak’ is developed to systematically identify genes recurrently affected by the genomic location of chromosomal CNA-associated breaks by a genome-wide approach, which can be applied to DNA copy number data obtained by array-Comparative Genomic Hybridization (CGH) or by (low-pass) whole genome sequencing (WGS). First, ‘GeneBreak’ collects the genomic locations of chromosomal CNA-associated breaks that were previously pinpointed by the segmentation algorithm that was applied to obtain CNA profiles. Next, a tailored annotation approach for breakpoint-to-gene mapping is implemented. Finally, dedicated cohort-based statistics is incorporated with correction for covariates that influence the probability to be a breakpoint gene. In addition, multiple testing correction is integrated to reveal recurrent breakpoint events. This easy-to-use algorithm, ‘GeneBreak’, is implemented in R (www.cran.r-project.org) and is available from Bioconductor (www.bioconductor.org/packages/release/bioc/html/GeneBreak.html).

Address of the bookmark: http://www.bioconductor.org/packages/release/bioc/html/GeneBreak.html