cbcb.umd.edu

metastats.cbcb.umd.edu

statistical methods for metagenomics

Software for metagenomic analysis. Detection of differentially abundant features - metagenomeSeq. Detection of differentially abundant features using metastats. We recommend you use metagenomeSeq. This site is maintained by Joseph Paulson.

metaphyler.cbcb.umd.edu

MetaPhyler

Estimating Bacterial Composition from Metagenomic Sequences. New version (05/23/2012): MetaPhylerV1.25.tar.gz. 252Mb). Allows training on your own data set; computes a confidence score for each classification. Here is a tutorial: metaphyler tutorial.pdf. Short Illumina reads ( NEW. MetaPhylerSRV0.115.tar.gz. Publication - Please Cite. Bo Liu, Theodore Gibbons, Mohammad Ghodsi, Todd Treangen, Mihai Pop. Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences. 21) Map metageno...

metapath.cbcb.umd.edu

MetaPath

Comparative Analysis of Metabolic Pathways in Metagenomics. One major and chalenging goal in metagenomics is to identify specific functional adaptations (signatures) of microbial communities to their habitats. Here we describe a powerful analytical method - MetaPath that can identify differentially abundant metabolic pathways in metagenomic datasets, relying on a combination of metagenomic sequence data and prior metabolic pathway knowledge (from KEGG). Lect Notes Comput Sci 2010, 6053: 101-112.

jazz.cbcb.umd.edu

Map of Jazz

Access the Map of Jazz. 1024x768 screem resolution or higher. Chrome 17.0, FireFox 10.0,S. Safari 5.0 or later. The Map of Jazz is an interactive website designed to explore collaborations among musicians in jazz history. Over the last one hundred years, jazz music has evolved as a dynamic network of interpersonal associations, both in the recording studio and on the concert stage. This project is funded by a Digital Humanities Grant from the National Endowment for the Humanities.

gage.cbcb.umd.edu

GAGE

GAGE is an evaluation of the very latest large-scale genome assembly algorithms. We have organized this "bake-off" as an attempt to produce a realistic assessment of genome assembly software in a rapidly changing field of next-generation sequencing. The main results of GAGE have now been published in the journal. GAGE: A critical evaluation of genome assemblies and assembly algorithms. Why do we need GAGE? How much sequencing coverage do I need for my genome project? Here are some differences:. We will c...

enterix.cbcb.umd.edu

Visualization tools for microbial genome alignments

Visualization Tools for Microbial Genome Alignments. The EnteriX servers allow comparative views of a reference bacterial or virus genome with sequences from several related organisms using two 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. Other organisms can be integrated upon request, and as sequence data become available. 18), 3486-96. [Medline].

blast.cbcb.umd.edu

Center for Bioinformatics and Computational Biology | CBCB

Center for Bioinformatics and Computational Biology. Center for Bioinformatics and Computational Biology. An interdisciplinary research institute supporting high-impact computing research across the College Park campus. If you would like to make a donation to the center click here. For a video on the mission and scope of CBCB. Feb 06, 2018. Mihai Pop Named Interim Director of UMIACS, Effective March 1. Jan 30, 2018. Ruppin Part of International Team Studying Interaction Between Aging Diseases and Cancer.

ardb.cbcb.umd.edu

ARDB-Antibiotic Resistance Genes Database

ARDB - Antibiotic Resistance Genes Database. Brief introduction to antibioitc resistance. Diams; Single Gene Annotation. Diams; Genome Annotation and Comparision. Diams; Genome Resistance Profiles Comparison. Diams; Mutation Detection. How to use GO terms to annotate resistance genes? Diams; Single Gene Submission. Diams; Batch Submission for Many Genes. Links to other sites. For help, collaboration, or others. Welcome to Antibiotic Resistance Genes Database Home Page. For large scale resistance genes an...

bowtie.cbcb.umd.edu

Center for Bioinformatics and Computational Biology | CBCB

Center for Bioinformatics and Computational Biology. Center for Bioinformatics and Computational Biology. An interdisciplinary research institute supporting high-impact computing research across the College Park campus. If you would like to make a donation to the center click here. For a video on the mission and scope of CBCB. Nov 22, 2016. CBCB scientist Erez Persi publishes a paper in Nature Communications on evolution of repeats in proteins. Oct 17, 2016. Oct 17, 2016. Oct 17, 2016. Oct 12, 2016.

spliceport.cbcb.umd.edu

Predictor and Splicing Features Analyser

SplicePort: An Interactive Splice Site Analysis Tool. Input sequences should be in FASTA. Format. Each sequence in the FASTA format begins with a single-line description, followed by one or several line of sequence data. The description line must begin with a greater-than symbol in the first column. The predictor uses a splice-site neighborhood of 80 nucleotides upstream and 80 nucleotides downstream for a constituent splice site. Upload Sequence File :. Max 30,000 bp).