NOVELTIES
ASPicDB is a database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm, and to the functional annotation of predicted isoforms (Martelli et al., Nucleic Acids Res 39:D80, 2011) Registration not required.
Click here for more informationsPublished on 2011-01-11 12:28:24
NONCODE is a database of all kinds of noncoding RNAs (except tRNAs and rRNAs). Registration not required.
Click here for more informationsPublished on 2011-01-08 05:53:44
The ICGC Goal is to obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. ICGC has been organized as an international effort to harmonize the large number of projects that are now, or shortly will be, underway that have the common aim of elucidating comprehensively the genomic changes present in many forms of cancer. Registration not required.
Click here for more informationsPublished on 2011-01-07 06:17:06
The HIV databases contain data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. Registration not required.
Click here for more informationsPublished on 2011-01-06 13:27:42
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.
Click here for more informationsPublished on 2011-01-03 05:15:37
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.
Click here for more informationsPublished on 2010-12-29 04:12:22
A wide collection of Proteomic tools hosted by the Swiss Proteomics Society
Click here for more informationsPublished on 2010-12-29 04:09:58
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.
Click here for more informationsPublished on 2010-12-17 02:59:52
PDQ® Cancer Information Summaries: Pediatric Treatment Registration not required.
Click here for more informationsPublished on 2010-12-16 14:14:16
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.
Click here for more informationsPublished on 2010-12-16 14:11:43
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.
Click here for more informationsPublished on 2010-12-13 12:10:07
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.
Click here for more informationsPublished on 2010-12-13 12:05:43
Various stand alone software for proteomics and genomics. Registration not required.
Click here for more informationsPublished on 2010-12-07 11:13:36
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.
Click here for more informationsPublished on 2010-12-07 11:05:25
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.
Click here for more informationsPublished on 2010-12-07 11:02:10
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.
Click here for more informationsPublished on 2010-12-07 10:56:58
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.
Click here for more informationsPublished on 2010-10-27 02:01:55
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.
Click here for more informationsPublished on 2010-10-27 02:00:35
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.
Click here for more informationsPublished on 2010-10-27 01:56:12
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.
Click here for more informationsPublished on 2010-10-27 01:55:15
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