Comparative Genomics Tools

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ECR Browser- The ECR Browser is a dynamic whole-genome navigation tool for visualizing and studying evolutionary relationships between vertebrate and non-vertebrate genomes. The tool is constantly being updated to include the most recently available sequenced genomes (currently: human, dog, mouse, rat, chicken, frog two pufferfish (Fugu and Tetraodon), zebrafish, and 6 fruitflies).
(http://ecrbrowser.dcode.org/)
      



Pattern Search - This specialized Vmatch server allows you to conduct pattern searches, i.e., searches for relatively short matches possibly interspersed with mismatches and indels. For example, if you designed a PCR primer (RT-PCR, or genomic PCR) to amplify your gene of interest, you may want to check if you primer sequences would likely cross-hybridize with other genes. You can use this tool to do just that. Upload your query sequence (pattern) file or paste your query sequence (pattern) into the large text field. Press the Search button to perform a search against the selected database sequences.
(http://www.plantgdb.org/PlantGDB-cgi/vmatch/patternsearch.pl)

 
Tracembler - allows you to do chromosome walks of trace sequences directly from NCBI's Trace Archive. This enables you to find your genes of interest in the most recent, pre-assembled sequence data.
( http://www.plantgdb.org/tool/tracembler/ )
         



MuSeqBox - a program for Multi-query Sequence Blast output examination.
( http://www.plantgdb.org/MuSeqBox/MuSeqBox.html ) 

dbERGE II - Database of experimental results on gene expression 
(http://globin.bx.psu.edu/dberge/)

EnteriX - VThis site allows comparative views of a reference genome (either E. coli K-12 or O157:H7, S. typhimurium LT2, S. typhi CT18 or S. paratyphi A) with sequences from several related bacteria using three different visualization tools.The Enteric server offers large-scale views of pairwise alignments, with point-and-click capabilities to retrieve related gene and alignment information. The Menteric tool displays nucleotide-level multiple alignments of the bacterial sequences, along with regulatory site annotations which the user interested in conservation and functional studies may want to explore further. The Maj viewer combines features of the previous two tools, and includes a zoom-in mechanism that allows examination both of the large-scale pairwise alignments and of the highest-scoring nucleotide-level multiple alignment in a sub-region selected by the user. 
(http://globin.cse.psu.edu/enterix/)

ETOPE - Evolutionary test of predicted exons.
Evolutionary test of predicted exons.This new tool allows you to test bilogical validity of computationally predicted exons using a simple evolutionary approach: the Ka/Ks test. this test takes advantage of the fact that in the vast majority of coding regions synonymous subtitutions (Ks) occur much more frequently than non-synonymous ones(Ka). Therefore for the majority of bilolgically valid sequences we expect Ka/Ks ratio to be smaller than 1.
(http://www.personal.psu.edu/users/z/u/zuz5/EEV/) 
 
 


GALA -  Genome alignment and annotation database .The GALA database(s) incorporate genomic annotation information with multi-species alignments to allow complex querying on publicly available sequence information.
We incorporate diverse annotation information including genes, SNPs, alignments, disease association and gene expression levels from multiple sources such as GenBank, Ensembl, The Whitehead Institute, and The Human Genome Browser.

Users may formulate simple or complex queries, by querying any field in the database individually, or by combining queries to refine and narrow the scope of the inquiry, respectively. Queries of the database allow a user to specify how much information they want to see. For instance, one can retrieve all information for a given region. Furthermore, one can identify characteristics that are common to distal loci such the amount of sequence conservation upstream of a specified gene family or SNP density that occurs more frequently than expected. Several options are given for textual output or visualization of the data. 
(http://gala.cse.psu.edu/) 

Galaxy - Metaserver for integrative analysis of genomic data. an interactive web tool for comparative genomics 
(http://g2.trac.bx.psu.edu/) 

HbVar - Database of human hemoglobin variants and thalassemias.This is a relational database of information about hemoglobin variants and mutations that cause thalassemia. The initial data came from Syllabi authored by Prof. Titus H.J. Huisman, Mrs. Marianne F.H. Carver, Dr. Erol Baysal, and Prof. Georgi D. Efremov. This information was converted to a database, and now new entries are added and old entries are corrected by our curators, Dr. Henri Wajcman, Dr. George Patrinos and Dr. Nick Anagnou. HbVar results from a collaboration among several investigators at Penn State University (USA), INSERM Creteil (France), and Boston University Medical Center (USA). Visit our query page or summary page to see the types of information available. 
(http://globin.bx.psu.edu/hbvar/) 

Mulan - Dynamic multi-sequence alignment and visualization.Dynamic multi-sequence alignment and visualization.dynamically and rapidly generates multiple sequence local alignments (MSLA).Mulan alignment engine consists of several data analysis and visualization schemes for high-throughput identification of functional coding and noncoding elements conserved across large evolutionary distances. Mulan (1) determines phylogenetic relationships among the input sequences and generates phylogenetic trees, (2) constructs graphical and textual alignments, (3) dynamically detects evolutionary conserved regions (ECR) in alignments, and (4) presents users with several visual display options for the generated conservation profiles. This tool is also able to implement the phylogenetic shadowing strategy for identifying slow-mutating elements in comparisons of multiple closely-related species (Ovcharenko et al. 2004a). In addition, Mulan is integrated with the MultiTF program that identifies evolutionarily conserved transcription factor binding sites (TFBS) shared by all analyzed species, allowing for the decoding of the sequence
structure of regulatory elements that are functionally conserved among different species.
(http://mulan.dcode.org.) 

PhenCode - Connects phenotype and clinical data in locus-specific databases with the PhenCode is a collaborative project to better understand the relationship between genotype and phenotype in humans. It connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions.Browser 
(http://globin.bx.psu.edu/mutation/) 

PipMaker / MultiPipMaker - Pairwise and multiple alignments of user-submitted DNA sequences. PipMaker computes alignments of similar regions in two DNA sequences. The resulting alignments are summarized with a ``percent identity plot'', or ``pip'' for short. MultiPipMaker allows the user to see relationships among more than two sequences. All pairwise alignments with the first sequence are computed and then returned as interleaved pips. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results. 
(http://pipmaker.bx.psu.edu/pipmaker/ )

PipHelper -PipHelper retrieves sequence as well as annotation data from the UCSC Genome Browser and generates sequence, repeats, and exons files suitable for further processing by PipMaker and MultiPipMaker. 
(http://pipmaker.bx.psu.edu/piphelper/)

                 



RP Scores - RP Scores are a computational tool to aid in the identification of putative regulatory sites of the human genome. Unlike tools based on searching for known transcription factor binding sites motifs, RP scores approach the problem from a comparative genomics perspective. These scores are computed from genome-wide alignments of the human with other organisms. In their current formulation, they exploit a mixture of conservation, composition and short-pattern structure information gathered from these alignments. We computed RP scores from 2-way alignments of human and mouse , and more recently from 3-way alignments of human, mouse, and rat . We also investigated the effectiveness of strategies comprising RP scores, pure conservation scores and binding sites searches, experimentally validating some of the resulting predictions .
(http://www.bx.psu.edu/projects/rp/)

ESPERR - Method for learning discriminative signals from multiple alignments
UCSC Genome Browser- Interactive browser for annotated genome sequences of human and other organisms This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project. Provides genome browser, gene sorter, blat search function, and publications.
(http://genome.ucsc.edu/) 

zPicture - Dynamic blastz alignment visualization. zPicture is a dynamic alignment and visualization tool that is based on blastz alignment program utilized by PipMaker. zPicture alignments can be automatically submitted to rVista 2.0 to identify conserved transcription factor binding sites.
(http://bioinfo.unice.fr/enseignements/www2005/tutoriels/outils/recherche_promoteurs/copie_de_pages_sites/zPicture.html)

http://ecrbrowser.dcode.org/)
        



VISTA Browser- WHOLE GENOME COMPARATIVE ANALYSIS OF THE HUMAN GENOME To explore comparative genomics we will use the VISTA Genome Browser from Ed Rubin's group at Lawrence Berkeley National Laboratory (LBNL) in Berkeley, Calif. For more information on the software and its authors, check out the paper listed in the resources section below. 
(http://pipeline.lbl.gov/cgi-bin/gateway2
       



BLAST Assembled Genomes - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
(http://130.14.29.110/BLAST/)              
             



PlantGDB GeneSeqer Online Server- GeneSeqer is a method to identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment.
(http://www.plantgdb.org/PlantGDB-cgi/GeneSeqer/PlantGDBgs.cgi)  


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