BOL: Related items

Collection of Graph Visualization tools !

Neel — Wed, 25 Jan 2023 02:57:42 -0600

Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation and sequence are separated.

https://fungidb.org/fungidb/app/downloads/Current_Release/GultimumBR650/

Address of the bookmark: https://pangenome.github.io/

SIMA C++ Implementation: Simultaneous Multiple Alignment of LC/MS Peak Lists

Neel — Thu, 23 Nov 2017 17:15:52 -0600

This is the c++ implementation for SIMA - Simultaneous Multiple Alignment of LC/MS Peak Lists. The package contains C++ source code as well as two binary files. The latter were tested under various operating systems, including Windows XP SP3 32bit, Windows Vista 32bit, Windows 2008 Server, Windows 7 32bit and 64bit, Ubuntu 10.04 64bit, Ubuntu 10.10 64bit, and gentoo AMD64.

The corresponding publication can be found here:

B. Voss*, M. Hanselmann*, B.Y. Renard, M.S. Lindner, U. Köthe, M. Kirchner, F.A. Hamprecht (2011). SIMA: Simultaneous Muliple Alignment of LC/MS Peak Lists, Bioinformatics 27(7):987-993. [doi] [techreport]

Address of the bookmark: https://hciweb.iwr.uni-heidelberg.de/hci/softwares/sima

MIX: Combining multiple assemblies from NGS data

Rahul Nayak — Tue, 08 May 2018 04:58:05 -0500

Mix is a tool that combines two or more draft assemblies, without relying on a reference genome and has the goal to reduce contig fragmentation and thus speed-up genome finishing. The proposed algorithm builds an extension graph where vertices represent extremities of contigs and edges represent existing alignments between these extremities. These alignment edges are used for contig extension. The resulting output assembly corresponds to a path in the extension graph that maximizes the cumulative contig length.

The Mix algorithm, approach and results were published in BMC bioinformatics : http://www.biomedcentral.com/1471-2105/14/S15/S16.

Address of the bookmark: https://github.com/cbib/MIX

FGENESH - Program for predicting multiple genes in genomic DNA sequences

BioStar — Thu, 20 Dec 2018 11:55:08 -0600

FGENESH is the fastest (50-100 times faster than GenScan) and most accurate gene finder available - see the figure and the table below. In recent rice genome sequencing projects, it was cited "the most successful (gene finding) program (Yu et al. (2002) Science 296:79) and was used to produce 87% of all high-evidence predicted genes (Goff et al. (2002) Science 296:79).

Address of the bookmark: http://www.softberry.com/berry.phtml?topic=fgenesh&group=help&subgroup=gfind

Kalign: fast multiple sequence alignment program for biological sequences.

BioStar — Fri, 01 Nov 2019 00:20:41 -0500

Kalign is a fast multiple sequence alignment program for biological sequences.

Align sequences and output the alignment in MSF format:

kalign -i BB11001.tfa -f msf  -o out.msf

Align sequences and output the alignment in clustal format:

kalign -i BB11001.tfa -f clu -o out.clu

Re-align sequences in an existing alignment:

kalign -i BB11001.msf  -o out.afa

Reformat existing alignment:

kalign -i BB11001.msf -r afa -o out.afa

Address of the bookmark: https://github.com/TimoLassmann/kalign

Mulan: MUltiple sequence Local AligNment and conservation visualization tool

Rahul Nayak — Thu, 20 Jul 2017 08:02:32 -0500

Mulan performs multiple (2 or more) sequence alignments with an efficient and rapid "full local" alignment strategy that ensures a recapitulation of evolutionary sequence rearrangements (such as inversions and reshuffling) in any of the species. It combines refine and tba tools to align either "draft" or "finished" quality sequences. Mulan provides a dynamic graphical interface to align and visualize conservation profiles for evolutionarily distant and closely related species.

Input formats, automated data upload from the UCSC Genome Browser, gene annotation, annotation of repetitive elements, and progress report were previously described in the zPicture instructions and we refer the users to these materials for more details. This introduction is mainly focused on some novel features unique to the Mulan.

Address of the bookmark: https://mulan.dcode.org/mulanInstructions.php

Tools to detect synteny blocks regions among multiple genomes

Jitendra Narayan — Mon, 16 Sep 2013 17:12:02 -0500

The synteny block (which etymologically means “on the same ribbon”) is a collection of contiguous genes located on the same chromosome. These block regions have mostly been preserved by genome rearrangements, and so synteny blocks from two related species (e.g., humans and mice) will be roughly similar but flipped around on the respective genomes. Ovcharenko et. al. define it as ‘any conserved sequence blocks, regardless of whether it encompasses multiple genes, an area containing single genes, or areas devoid of known genes to be considers as synteny block as long as there is conservation at the sequence level. Today, however, biologists usually refer to synteny as the conservation of blocks of order within two sets of chromosomes that are being compared with each other. This concept can also be referred to as shared synteny. The NHBLI/NCBI Glossary define synteny as “Two genes which occur on the same chromosome are syntenic; however, syntenic genes may or may not be "linked."

Now a day, geneticists have developed a language of their own. They are pouring lots of money and energy to read the entire genomic text and understand the gods own code ATGC. It is somewhat fascinating, not only for geneticist but also for non-biologist to know that there are several conserved blocks in genome which remain conserved over hundreds of millions of years. There have been several researches on conserved blocks and non-conserved regions to understand the mechanism and importance of all these regions (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/). The finding indicates conservation and rearrangements of certain evolutionary important genes play an important role in evolution/adaptive changes (http://www.nature.com/nature/journal/v491/n7424/abs/nature11622.html https://academic.oup.com/gbe/article/8/8/2442/2198198/Novel-Insights-into-Chromosome-Evolution-in-Birds , http://science.sciencemag.org/content/346/6215/1311).

But the puzzle remains open, how to correctly define the synteny (presence of two or more genes on the same chromosome) and conserved synteny (presence of two or more genes on chromosome of each of the two species) on several genomes.

Figure: Image generated with Evolution Highway (EH) tool http://eh-demo.ncsa.illinois.edu/

Keeping the new approach to define conserved synteny in mind there have been various algorithms developed to identify the conserved homologous synteny blocks (HSB) amongst species. Some of them which were commonly used for synteny detections are:

SyntenyTracker ( http://www-app.igb.uiuc.edu/labs/lewin/donthu/Synteny_assign/html/),

SyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies.

CoGe (http://genomevolution.org/CoGe/SynFind.pl )

Satsuma (http://evomics.org/learning/genomics/satsuma/)

Cinteny (http://cinteny.cchmc.org/) ,

Cinteny server can be used for finding regions syntenic across multiple genomes and measuring the extent of genome rearrangement using reversal distance as a measure.

OrthoCluster (http://krono.act.uji.es/noticias/orthocluster-a-new-tool-for-mining-syntenic-blocks)

A new tool for mining syntenic blocks in comparative genomics

SynMap (http://genomevolution.org/wiki/index.php/SynMap),

SyMAP (http://www.symapdb.org/)

SyMAP (Synteny Mapping and Analysis Program) v4.0 is an automated system for identifying and displaying genome synteny alignments. The genomes may be represented by sequenced chromosomes (pseudomolecules), by draft sequence contigs, or by FPC physical maps (with BAC-end or marker sequence).

http://genomevolution.org/CoGe/SynMap.pl

RegionMiner (http://www.genomatix.de/online_help/help_regionminer/orthologous.html)

SyntenyMiner is being developed as an application to visualize and interrogate comparisons among multiple complete genome sequences. http://syntenyminer.sourceforge.net/

AutoGRAPH ( http://autograph.genouest.org/),

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.

SynChro(http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

SynChro is a tool designed to define conserved synteny blocks. It reconstructs synteny blocks between pairwise comparison of multiple genomes. The reconstructed synteny blocks may overlap each other, be included in one another or duplicated due to micro-rearrangements.

SyntenyView ( http://www.cbs.dtu.dk/dtucourse/cookbooks/nikob/exercises/gf1_output_5.html),

Ensembl 'SyntenyView' shows conservation of large-scale gene order between species pairs. A brief summary of the calculation method appears at the bottom of this help page. The left of a 'SyntenyView' page displays a diagram of chromosomes with blocks of conserved synteny. The right of a page shows homology matches between individual genes within syntenic blocks.

SynBrowse ( http://www.synbrowse.org/),

SynBrowse (Synteny Browser) is a generic sequence comparison tool for visualizing genome alignments both within and between species. It is intended to help scientists study and analyze synteny, homologous genes and other conserved elements between sequences. This software is useful in studying genome duplication and evolution. It can also aid in identifying uncharacterized genes, putative regulatory elements and novel structural features of study species by comparing to a well annotated reference sequence, thus enabling genome curators to refine and edit annotations of species that have incomplete genome annotations.

Sibelia (http://arxiv.org/abs/1307.7941).

A comparative genomic tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms.

GSV (http://cas-bioinfo.cas.unt.edu/gsv/homepage.php)

Genome Synteny Viewer allows users to upload files which contain synteny regions between two or more genomes and interactively visualize the synteny between them. GSV also allows users to upload annotation files to visualize annotated regions in addition to synteny regions.

MicroSyn (http://www.lgm.upmc.fr/CHROnicle/SynChro.html)

MicroSyn software as a means of detecting microsynteny in adjacent genomic regions surrounding genes in gene families. MicroSyn searches for conserved, flanking colinear homologous gene pairs between two genomic fragments to determine the relationship between two members in a gene family.

SynOrth (http://synorth.genereg.net/)

Synorth [s n ôrth], named in combination of "synteny" and "ortholog", is designed for the study of evolutionary changes of genomic regulatory blocks (GRBs) in vertebrate genomes, and especially the changes following the whole-genome duplication in teleost fish, by tracing the ortholog genes gain and loss in ancient synteny blocks.

SyDiG (http://www.ncbi.nlm.nih.gov/pubmed/21441096)

Uncovering Synteny in Distant Genomes.

MapSynteny (http://www.automatizacionysistemas.com/download.html)

MapSynteny is a macro in MS Excel® able to create images to show the relationship between genetic maps and large sequences (scaffolds, chromosomes, BACs, etc.). Based on tab – delimited BLAST results and some formulas, a suitable image of syntenic relationships or physical mapping can be obtained. http://www.automatizacionysistemas.com/Poster_MapSynteny.pdf

One of the best synteny tutorial for beginer @ http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

Reference:

http://www.nature.com/scitable/topicpage/synteny-inferring-ancestral-genomes-44022

http://www.nature.com/nature/journal/v491/n7424/full/nature11622.html

http://en.wikipedia.org/wiki/Synteny

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675965/

Murasaki

Anjana — Fri, 30 Sep 2016 10:22:30 -0500

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

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

MCscan

Bulbul — Thu, 22 Dec 2016 03:53:58 -0600

MCscan is a computer program that can simultaneously scan multiple genomes to identify homologous chromosomal regions and subsequently align these regions using genes as anchors. This is the toolset for generating the synteny correspondences in Plant Genome Duplication Database. It is intended as an easy-to-use and quick way to identify conserved gene arrays both within the same genome and across different genomes.

More at http://chibba.agtec.uga.edu/duplication/mcscan/

Address of the bookmark: http://chibba.agtec.uga.edu/duplication/mcscan/

orthodotter: Synteny plots (oxford grid)

Jit — Wed, 09 Aug 2017 07:16:16 -0500

orthodotter -h
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orthodotter - Plot orthologous genes on an oxford grid.
       -f      : input file, containing orthologous genes, default is stdin
                       species chr-name start end species chr-name start end
       -toPlot  : give the x and y sets and the color separated by double-dots,
                       for example set1:set2:red will plot set1 on x, set2 on y with
                       red points. Could give several -toPlot arguments.
                       To launch the clustering of dots, use extra-option 1=dist,min_nb_genes
                       where dist is the minimal distance (euclidian) between two points and min_nb_genes the minimal
                       number of genes in a cluster to be valid.
       -o      : output file, default is stdout
       -x       : resolution of x axis, default is 600
       -y       : resolution on y axis, default is 600
       -r       : radius of circle representing orthologous genes
       -format       : could be png, gif, jpg, pdf or ps. Default is png.
       -fg           : foreground color, default is black
       -bg           : background color, default is transparent
       -fSize   : fontSize, default is 1
       -filter       : check chromosome names
       -h            : help
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orthodotter -f Vigne_Banane.ortho -toPlot Vigne:Banane:black:1=10,5 -x 1200 -y 1200 -bg white -o Vigne_vs_Banane.png > Vigne_vs_Banane.clusters
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Address of the bookmark: https://github.com/institut-de-genomique/orthodotter