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RNA( 10/16 )

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CentroidFold

Summary CentroidFold is a software to predict RNA second structure and common second structure. A benchmark test shows it performs better than Mfold and RNAfold.
Data type RNA

HEAT

Summary H-InvDB Enrichment Analysis Tool (HEAT) is a data-mining tool for automatically identifying features specific to a given human gene set. HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts. This technique is called Gene Set Enrichment Analysis (GSEA), and is popularly used in analyzing results of microarray experiments. Fisher's exact probability is used in statistical tests of HEAT.
Data type Annotation

Idiographica

Summary Idiographica is a web server for you to create your own idiogram. Please fill the following web form and click on the submit button. The Idiographica server will send you an email to notify the completion of the idiogram creation task. You can use the generated idiograms without any restriction or obligation. (cited from the original site)
Data type Chromosome

LAST

Summary LAST is a software for comparing and aligning sequences, typically DNA or protein sequences. LAST is similar to BLAST, but it copes better with very large amounts of sequence data. It can also report probabilities for every pair of aligned letters, indicating the reliability of each pairing.
Data type DNA-sequence ,RNA, protein, user-defined alphabet.

MXSCARNA

Summary MXSCARNA (Multiplex Stem Candidate Aligner for RNAs) is a multiple alignment tool for RNA sequences using progressive alignment based on pairwise structural alignment algorithm of SCARNA.
Data type RNA (RNA sequence)

Murlet

Summary Murlet is a multiple alignment tool for RNA sequences using iterative alignment based on Sankoff's algorithm with sharply reduced computational time and memory. This was developed by Computational Biology Research Center (CBRC), AIST.
Data type RNA

PMID-Extractor

Summary PMID-Extractor allows a user to obtain PubMed IDs (PMIDs) from PDF files or text format files of journal paper in your hand. From Digital Object Identifiers (DOIs, http://en.wikipedia.org/wiki/Digital_object_identifier) or text information (e.g. titles) in the first page of each files, To start using PubMedScan (http://medals.jp/pubmedscan/), a paper recommender, PMIDs are required to specify the users’ interest. That is the main usage of PMID-Extractor.
Data type Journal

RNAmine

Summary
Data type RNA

Rfold

Summary
Data type RNA

SAMURAI

Summary Gene expression networks have different gene components depending on the cell types. SAMURAI is a tool for finding such minimal functional units of genes called modules from large-scale gene expression data. Modules are searched against by an ultra fast and exhaustive biclustering method using a closed itemset mining algorithm.
Data type Gene expression
Per 10 Results