NOVELTIES
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.
Click here for more informationsPublished on 2010-10-26 15:02:21
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.
Click here for more informationsPublished on 2010-10-26 14:59:58
Automated Identification of Prophage Regions in Complete Bacterial Genome Sequences Registration not required.
Click here for more informationsPublished on 2010-10-26 14:58:45
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.
Click here for more informationsPublished on 2010-10-26 14:56:44
The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts for the distance between neighboring genes on each DNA molecule and the BLAST E-value score between homologs, maximally scoring chains of ordered gene pairs are computed and reported. This algorithm can be used to mine large evolutionary conserved regions of genomes between two organisms. Alternatively, by examining colinear sets of homologous genes found within a single genome, segmental genome duplications can be revealed. This software distribution includes both the DAGchainer utility and a Java-based graphical interface that allows the inputs and outputs to be navigated and interrogated dynamically. Registration not required.
Click here for more informationsPublished on 2010-10-26 14:53:44
Lucy was designed and written at The Institute for Genomic Research (TIGR, now the J. Craig Venter Institute), and it has been used here for several years to clean sequence data from automated DNA sequencers prior to sequence assembly and other downstream uses. The quality trimming portion of lucy makes use of phred quality scores, such as those produced by many automated sequencers based on the Sanger sequencing method. As such, lucy’s quality trimming may not be appropriate for sequence data produced by some of the new “next-generation” sequencers. Lucy is available in the form of a software download only. I currently have no plans to create an open-source community development project for lucy. If you think that would be valuable, please contact me about it. In the meantime, the download package includes the full source code, so feel free to customize it for your environment. Registration not required.
Click here for more informationsPublished on 2010-10-26 14:46:50
Elvira is a set of tools and procedures designed for high throughput assembly of small genomes such as viruses. The name Elvira stands for Executive for Large-scale VIRal Assembly. Elvira is particularly suitable in situations where any of the following occur: 1. Sequences must be individually trimmed against specific primers. 2. Sequences must be trimmed against degenerate primers. 3. Assemblies need to be explicitly partitioned based on sequence origin. The Elvira package includes some well-known components, including 1. Elvira, the genome assembly pipeline for unix. 2. Lemur, the element tracking and manipulation web app. 3. GLK, the database schema and associated perl module. This software was developed at TIGR where it contributed to the sequencing and publication of thousands of viral genomes. This software makes use of the AMOS package of genome assembly tools. This software uses perl, PHP, and AJAX. Registration not required.
Click here for more informationsPublished on 2010-10-26 14:31:10
This is a software library to run the JCVI barcode deconvolution pipeline using Sun Grid Engine, or optionally without the use of a grid. Registration not required.
Click here for more informationsPublished on 2010-10-26 14:30:29
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Long sequences assembling from SourceForge
Category: Sequencing and assembly software
Celera Assembler : scientific software for biological research. Celera Assembler is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. It' a whole genome assembler originally developed at Celera Genomics for the assembly of the human genome. CeleraAssembler is now an open-source project at SourceForge. The code is actively maintained by researchers at CBCB and the Venter Institute (formerly known as TIGR, The Institute for Genomic Research). Registration not required.
Click here for more informationsPublished on 2010-10-26 14:28:35
Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA. Registration not required.
Click here for more informationsPublished on 2010-10-25 15:03:26
R is a language and environment for statistical computing and graphics. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, ...) and graphical techniques, and is highly extensible. R is developed by Robert Gentleman and Ross Ihaka. Registration not required.
Click here for more informationsPublished on 2010-10-22 12:01:49
This screen computes several statistics from a table whose row and column categories form logically ordered sequences. It can accommodate a table with up to five rows and/or five columns Registration not required.
Click here for more informationsPublished on 2010-10-22 11:22:14
This page computes various statistics from a 2-by-2 table. It will calculate the Yates-corrected chi-square, the Mantel-Haenszel chi-square, the Fisher Exact Test, and other indices relevant to various special kinds of 2-by-2 tables. Registration not required.
Click here for more informationsPublished on 2010-10-21 12:41:47
This page contains links to free software packages that you can download and install on your computer for stand-alone (offline, non-Internet) computing. Registration not required.
Click here for more informationsPublished on 2010-10-21 12:35:58
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MicroArray Genome Imaging and Clustering Tool (MAGIC Tool)
Category: DNA microarray software
MAGIC Tool is an integrated microarray data analysis free software with open source. Registration not required.
Click here for more informationsPublished on 2010-10-21 12:23:27
VisANT (from Bosto Univeristy) is a lightweight network visualization tool able to run as a browser-based applet or as a standalone Java program. Registration not required.
Click here for more informationsPublished on 2010-10-21 11:52:08
CellProfiler is a free open-source software for high-throughput image-based cell profiling using fluorescence microscopy. It is designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. CellProfiler Analyst is free open-source software for exploring and analyzing large, high-dimensional image-derived data. It includes machine learning tools for identifying complex and subtle phenotypes. Registration not required.
Click here for more informationsPublished on 2010-10-20 12:04:41
Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, it is possible edit pages in Proteopedia. Registration not required.
Click here for more informationsPublished on 2010-10-20 11:45:36
The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. It is commonly used by molecular biologists, for teaching, and for program and algorithm testing. Registration not required.
Click here for more informationsPublished on 2010-10-20 11:08:14
JaMBW, the Java based Molecular Biologist's Workbench, is an online platform that had been put together in order to try to give a free access to the exploitment of the most common bioinformatic operations that a molecular biologist currently has. The peculiar aspect of JaMBW, however, is to take advantage of the foremost developments in computer science in order to deliver information in a way simple to use. Registration not required.
Click here for more informationsPublished on 2010-10-19 12:40:33
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