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NOVELTIES

modENCODE logo
Category: Model organisms
Subcategories: Worm , Drosophila , Encode

The National Human Genome Research Institute (NHGRI) model organism ENCyclopedia Of DNA Elements (modENCODE) Project will try to identify all of the sequence-based functional elements and the genome-wide patterns of regulatory interactions in the Caenorhabditis elegans and Drosophila melanogaster genome. Registration not required.

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Published on 2011-01-03 05:15:37
DAVID logo

The Database for Annotation, Visualization and Integrated Discovery (DAVID ) v6.8 comprises a full Knowledgebase update to the sixth version of our original web-accessible programs. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

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Published on 2010-12-29 04:12:22
ExPASy Proteomics Server logo

A wide collection of Proteomic tools hosted by the Swiss Proteomics Society

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Published on 2010-12-29 04:09:58
Rfam logo
Category: RNA miscellanea
Subcategories: Janelia

Rfam is a collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format. In conjunction with the Infernal software package, Rfam covariance models (CMs) can be used to search genomes or other DNA sequence databases for homologs to known structural RNA families. Registration not required.

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Published on 2010-12-17 02:59:52
PDQ® Cancer Treatment - Pediatrics (NCI) logo

PDQ® Cancer Information Summaries: Pediatric Treatment Registration not required.

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Published on 2010-12-16 14:14:16
Infernal logo

Infernal (inference of RNA alignments) is a software package for searching DNA sequence databases for RNA structure and sequence similarities. It allows you to make consensus RNA secondary structure profiles, and use them to search nucleic acid sequence databases for homologous RNAs, or to create new structure-based multiple sequence alignments. Registration not required.

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Published on 2010-12-16 14:11:43
OCHeM- Organic Chemistry logo
Category: Other tutorials

This graphics-rich site from Thomas Poon and Bradford Mundy More provides virtual flash cards with a dozen animated tutorials cover everything from drawing chemical structures, to the basics of mass spectrometry, to the reactions of aldehydes and ketones. Registration not required.

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Published on 2010-12-13 12:10:07
Virtual Textbook of Organic Chemistry logo
Category: Other tutorials

This comprehensive organic chemistry Web text from William Reusch of Michigan State University in East Lansing can enlighten not only students but also working chemists who need a refresher on the details of a particular reaction (Science 303, 115,2004) Registration not required.

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Published on 2010-12-13 12:05:43
COmics logo
Computational Omics Lab

Various stand alone software for proteomics and genomics. Registration not required.

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Published on 2010-12-07 11:13:36
msInspect logo
Hosted buy GitHub

msInspect is an open source application written in Java that allows you to process and view mass spectrometry (MS1) data in an mzXML file. You can inspect data, identify peptide features, generate peptide arrays using data from multiple runs, and export data to external applications for further analysis and collaboration. Registration not required.

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Published on 2010-12-07 11:05:25
MzMine logo

MZmine 2 is an open-source software for mass-spectrometry data processing, with the main focus on LC-MS data and with the main goal to provide a user-friendly, flexible and easily extendable framework with a complete set of modules covering the entire LC-MS data analysis workflow. Registration not required.

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Published on 2010-12-07 11:02:10
MSight logo

MSight, created by the Proteome Informatics Group, was specifically developed for the 2-D representation of mass spectra along with data from the separation step. The software allows graphical exploration inside huge dataset and gives the scientist access to information that previously was hidden. Registration required.

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Published on 2010-12-07 10:56:58
Maq logo
From SourceForge

Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is previously known as mapass2. Registration not required.

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Published on 2010-10-27 02:01:55
MACS logo
Froma Dana-Farber Cancer Institute

Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, is publicly available open source, and can be used for ChIP-Seq with or without control samples. Registration not required.

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Published on 2010-10-27 02:00:35
Edena logo

Edena (Exact DE Novo Assembler) is an assembler dedicated to process the millions of very short reads produced by the Illumina Genome Analyzer. Edena is based on the traditional overlap layout paradigm. All exact overlaps between any pair of reads are computed and structured in a graph (overlap step). Basically, the reads are indexed in a prefix array and overlaps are revealed by dichotomic search in the arrays. The graph is then analyzed to remove transitive and spurious edges (layout step). Finally, contigs that can be assembled following unambiguous path in the graph are given as output. Edena allows to produce contigs of several kbp with a near full coverage of the bacterial genome being sequenced. Registration not required.

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Published on 2010-10-27 01:56:12
Bowtie logo
Short reads aligner SourceForge

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end). Registration not required.

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Published on 2010-10-27 01:55:15
Magnolia logo

Since it has been an obligation to submit microarray experiment data to public repositories for publishing the experimental results, collecting and storing the data is an essential step in microarray study. Implemented with H2 DBMS as the backend storage, Magnolia provides PFGRC array users with a series of intelligent entry form to collect the information or parameters of experiment, bio-source, sample, probe, slide, scan, expression, and normalization, which is MIAME compliant (Minimal Information About a Microarray Experiment; (Brazma et al., 2001)). The collected data are saved to a relational database defined by users and can be modified easily with a set of corresponding edit pages. Working as an exporter, Magnolia can write out the entered data into GEO sample and series files in SOFT format that is acceptable by GEO, so that the files can be submitted to GEO directly. Magnolia also serves as a platform for launching other data manipulation tools, such as SQL Query Window to report the entered data, Slide Annotation to load array annotation file downloaded from PFGRC site into the database, and Database Schema to present the relationships among the tables. Registration not required.

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Published on 2010-10-26 15:02:21
Sybil logo
From SouceForge

Sybil is a web-based software package for comparative genomics. It was developed by the Bioinformatics department at The Institute for Genomic Research (TIGR) and development continues at the J. Craig Venter Institute and Institute for Genome Sciences (IGS) at the University of Maryland Baltimore's School of Medicine. The project has been funded by a variety of sources including: The National Institute of Allergy and Infectious Diseases (NIAID) as part of the NIAID Bioinformatics Resource Centers (BRC) for Biodefense and Emerging or Re-Emerging Infectious Diseases and PATH an organization supporting research in Streptococcus and Neisseria vaccine development. While still under development, several of the Sybil tools have been used internally at TIGR, the JCVI and IGS by research projects that involve comparative genome analysis. See the SCREENSHOTS section below for examples of the types of analyses and displays that the system currently supports, or follow the link to the Demos page to interact with a live (albeit scaled-down) version of the system, running on a demonstration database that contains genome sequences, annotation, and comparative data from ten Streptococcus pneumoniae genomes. If you have any questions or suggestions, please contact us using the sybil-info mailing list. Registration not required.

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Published on 2010-10-26 14:59:58
PhageFinder logo
From SourceForge

Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences Registration not required.

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Published on 2010-10-26 14:58:45
MUMmer logo
From SourceForge

MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences. The original MUMmer system, version 1.0, is described in our 1999 Nucleic Acids Research paper. Version 2.1 appeared a few years later and is described in our 2002 Nucleic Acids Research paper, while MUMmer 3.0 was recently described in our 2004 Genome Biology paper. We have also developed a GPU accelerated version of MUMmer called MUMmerGPU. Registration not required.

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Published on 2010-10-26 14:56:44
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