BOL: Related items

Rosalind Bioinformatics problems !!!

Abhi — Thu, 18 Dec 2014 10:32:48 -0600

Rosalind is a platform for learning bioinformatics and programming through problem solving. Take a tour to get the hang of how Rosalind works.

http://rosalind.info/problems/list-view/

Address of the bookmark: http://rosalind.info/problems/list-view/

LASTZ

Abhi — Mon, 18 Apr 2016 04:41:55 -0500

LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.

More at http://www.bx.psu.edu/~rsharris/lastz/

Thesis: http://www.bx.psu.edu/~rsharris/rsharris_phd_thesis_2007.pdf

Address of the bookmark: http://www.bx.psu.edu/~rsharris/lastz/

Ensembl comparative genomics resources

Jitendra Narayan — Sun, 28 Feb 2016 17:10:20 -0600

The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available.

Database URL: http://www.ensembl.org.

Address of the bookmark: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4761110/

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

AccNET

Jitendra Narayan — Fri, 07 Oct 2016 05:22:11 -0500

AccNET is a Perl application that presents a new way to study the accessory genome of a given set of organisms. Using the proteomes of these organisms, AccNET create a bipartite network compatible with common network analysis platforms. AccNET collects phylogenetic and functional information in a network improving the analysis capability. Networks offer a new perspective of organism organization through elements acquired by horizontal gene transfers and not constricted by hierarchical structures.

More at https://www.youtube.com/watch?v=vdGuy1GAJrQ

Address of the bookmark: https://sourceforge.net/projects/accnet/

SATSUMA : Highly sensitive whole-genome synteny alignments.

Jit — Fri, 13 May 2016 05:25:26 -0500

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences. Satsuma does not require any pre-processing, such as repeat masking, since it will automatically detect ambiguous mappings.

Satsuma has parallelization built-in and is designed to run on multi-core architectures. The run-time for aligning two bird-size genomes (~1.2 Gb) is around two days on 24 CPUs.

You can find the manual here.
Download the latest source code from here.
Stable versions can also be downloaded from the Broad Institute's web site.

An incomplete list of questions and answers (yes, these have really been asked by our users! Please feel free to add your own by e-mailing us) is here.

If you use Satsuma in your research, please cite:
Grabherr, M. G., Russell, P., Meyer, M., Mauceli, E., Alföldi, J., Di Palma, F., & Lindblad-Toh, K. (2010). Genome-wide synteny through highly sensitive sequence alignment: Satsuma. Bioinformatics, 26(9), 1145-51.

Tutorial at http://evomics.org/learning/genomics/satsuma/

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

Hagfish - assess an assembly through creative use of coverage plots

Abhi — Fri, 20 May 2016 19:08:17 -0500

Hagfish is a tool that is to be used in data analysis of Next Generation Sequencing (NGS) experiments. Hagfish builds on the concept of coverage plots and aims to assist (amongst others) in quality control of de novo genome assembly or identification of structural variation in a genome re-sequencing experiment.

Hagfish requires a reference sequence and a paired end re-sequencing data set. Hagfish has more power the larger the insert size of the paired end library is.

Quick links: Installation,Operation, Read mappers, Hagfish scripts, Hagfish plots

Address of the bookmark: https://github.com/mfiers/hagfish

Samtools Primer !!

Jit — Thu, 23 Jun 2016 07:18:17 -0500

SAMtools: Primer / Tutorial by Ethan Cerami, Ph.D.

keywords: samtools, next-gen, next-generation, sequencing, bowtie, sam, bam, primer, tutorial, how-to, introduction
Revisions

    1.0: May 30, 2013: First public release on biobits.org.
    1.1: July 24, 2013: Updated with Disqus Comments / Feedback section.
    1.2: December 19, 2014: Multiple updates, including:
        Updated to use samtools 1.1 and bcftools 1.2.
        Updated usage for bcftools.

About

SAMtools is a popular open-source tool used in next-generation sequence analysis. This primer provides an introduction to SAMtools, and is geared towards those new to next-generation sequence analysis. The primer is also designed to be self-contained and hands-on, meaning that you only need to install SAMtools, and no other tools, and sample data sets are provided. Terms in bold are also explained in the glossary at the end of the document.

Address of the bookmark: http://biobits.org/samtools_primer.html

TGNet

Shruti Paniwala — Wed, 24 Aug 2016 05:36:36 -0500

Recent technological progress has greatly facilitated de novo genome sequencing. However, de novo assemblies consist in many pieces of contiguous sequence (contigs) arranged in thousands of scaffolds instead of small numbers of chromosomes. Confirming and improving the quality of such assemblies is critical for subsequent analysis.

Visualization and quality assessment of de novo genome assemblies

Citation

This software is fully described in the paper:
Riba-Grognuz, Keller, Falquet, Xenarios & Wurm (2011) Visualization and quality assessment of de novo genome assemblies.

In brief, our scripts create Cytoscape files to visualize transcript evidence that suggests adjacency between scaffolds and contigs.

Software requirements

BLAT (tested with Standalone BLAT v. 32×1). Source Binaries .
Cytoscape (tested with versions 2.7.0, 2.8.2)
a UNIX machine (tested on Mac OS X 10.6 and CentOS 4.6)

Address of the bookmark: https://github.com/ksanao/TGNet

Gene Finding and Predictions

Poonam Mahapatra — Fri, 26 Aug 2016 07:26:27 -0500

In this exercise, a previously annotated gene will be used to measure the accuracy of different gene finding approaches. GRAIL, GENSCAN, geneid, FGENESH, GenomeScan, GrailEXP and GENEWISE will be used to annotate the sequence. Both search by signal, content and homology (protein and cDNA sequences) methods will be employed in order to improve the ab initio results. Weak conservation of Start codons will lead to wrong prediction of initial exons in most cases.

http://genome.crg.es/courses/Bioinformatics2003_genefinding/

Address of the bookmark: http://genome.crg.es/courses/Bioinformatics2003_genefinding/