Synteny block identification aims to identify homologous chromosomal regions and relations between genomes. The identification of conserved syntenic regions enables discovery of predicted locations for orthologous and homeologous genes, even when no such gene is present. This capability means that synteny-based methods are far more effective than sequence similarity-based methods in identifying true-negatives, a necessity for studying gene loss and gene transposition.
A statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach.
Screens a set of synteny blocks to retain only those compatible with a user specified ploidy relationship between two genomes. QUOTA-ALIGN can be used to solves the problem of selecting a subset of synteny blocks by using the expected quota known a priori from the inferred occurrences of past whole genome duplication (WGD) events and permits the user to identify subset of synteny blocks more relevant to a specific evolutionary event. QUOTA-ALIGN can be used to (i) reduce the block screening task to a binary integer programming (BIP) problem, which is novel, and (ii) providing an efficient software pipeline starting from all-against-all BLAST to the screened synteny blocks with dot plot visualizations.
Incorporates a hierarchical taxonomic tree allowing access to all completely sequenced prokaryotes. SyntTax allows to choose single or multiple organisms on the basis of their lineage by selecting the corresponding rank nodes in the tree. This web tool produces syntenies by providing prompt access to the taxonomic relationships connecting all completely sequenced microbial genomes. It can be used to resolve some conserved complex gene clusters.
Assists the manual curation of local synteny information. SynBlast focuses on individual loci of interest. It provides researchers with detailed information on all plausible homologs and their genomic context. This tool can automate the retrieval of proteins from syntenic regions and comparison of assignments with existing annotations the Ensembl system and databases that were chosen as standard reference sources.
Allows visualization of conservation of gene adjacency in many prokaryotic genomes. SynteView displays synteny comparison between a reference genome (choosen by the user) and a set of genomes choosen among a total of 600 prokaryotic genomes stored in SynteBase, a dedicated relational database. This application was developed as a web service and provides a local access mode.
Identifies statistically significant synteny blocks in pairwise comparisons of eukaryote genomes. Compared to previous methods, PhylDiag uses gene trees to define gene homologies, thus allowing gene deletions to be considered as events that may break the synteny. PhylDiag also accounts for gene orientations, blocks of tandem duplicates and lineage specific de novo gene births. Starting from two genomes and the corresponding gene trees, PhylDiag returns synteny blocks with gaps less than or equal to the maximum gap parameter gap(max). This parameter is theoretically estimated, and together with a utility to graphically display results, contributes to making PhylDiag a user friendly method. In addition, putative synteny blocks are subject to a statistical validation to verify that they are unlikely to be due to a random combination of genes.
Constructs and publishes websites for synteny block analyses by exploiting user’s genome sequences or synteny block definitions. mySyntenyPortal provides through an offline standard-alone application a unified management system to achieve synteny-based analyses and manage/publish websites connected to databases constructed with the command line interface. Users can selectively publish or unpublish a website connected to a specific database.
Enumerates conserved blocks that are centered in small components of a given input DNA element and ranks them according to a probabilistic ranking score. RAGB is based on interrogating a given reference DNA element from a specific genome for subsets of genes that are conserved as proximity blocks across other microbial genomes. This tool will be useful for future studies of gene-block evolution.
A fast and easy-to-use program for the identification of synteny blocks among multiple genomes. OrthoCluster allows users to identify synteny blocks that contain different types of mismatches, and to decide whether they require conservation of gene orientation and conservation of gene order within the blocks. OrthoCluster can also be used to find duplicated blocks within genomes. Although genes and their correspondence are usually used as input for OrthoCluster, in fact, OrthoCluster can be applied using any type of markers as input as long as their relationships can be established.
Assists user in gene team problem. This algorithm has a time complexity independent of , since it does not rely on examining every combination of genomes. This method is specially developed for maximal gene teams. The presented algorithm can be used as an effective tool for large scale genome analyses. It was implemented by checking every pair of patterns in a brute force manner.
Allows multiple synteny determination and visualization between user’s genomic data and/or published plant genome data. MultiSyn allows users to set regions of interest of species against the 18 plants provided in the webtool by choosing a species, chromosome, and input locus information at the start and end positions. It aims to aid evolutionary analysis by displaying multiple synteny. The tool provides a convenient means for biologists to analyze their sequence of interest.
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. Sibelia is useful in finding: (1) shared regions, (2) regions that present in one group of genomes but not in others, (3) rearrangements that transform one genome to other genomes. In version 2, Sibelia works with multiple strains of bacteria and partitions their genomes into synteny blocks — blocks of highly conserved regions among all compared genomes. It represents genomes in Circos pictures or interactive forms.
Builds images to underline the relationship between genetic maps and large sequences. MapSynteny consists of a macro model in Microsoft Excel. It is useful for synteny analysis or physical mapping. This tool can serve for the macro-assembly of scaffolds to give relationships at the chromosome level.
Computes conserved gene clusters through N-genomes comparison in two phases. MCMuSeC allows to detect conserved gene clusters under flexible evolutionary constraints in a large number of genomes. The combined algorithmic and statistical methods provide a rigorous framework for systematically studying evolutionary constraints of genomic contexts.
Detects 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. The colinearity of homologous pairs is controlled by a statistical distance function. As a result, gene duplication history can be inferred from the output independent of gene sequences. MicroSyn was designed for both experienced and non-expert users with a user-friendly graphical-user interface.
An automated tool for the identification of homologous synteny blocks (HSBs) between genomes that tolerates errors common in radiation-hybrid (RH) comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution. Compared to the AutoGRAPH synteny block definition tool, SyntenyTracker demonstrated higher quality of HSB definition in those cases when proper definition of an HSB was dependent on simultaneous analysis of several reference and target chromosomes.