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, a paper recommender, PMIDs are required to specify the users' interest. That is the main usage of PMID-Extractor. |
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| Data type | Journal |
PSTAG
| Summary | PSTAG (Pair Stochastic Tree Adjoining Grammars) is for RNA sequences including pseudoknotted structures.The program based on PSTAGs is the first grammar-based and practically executable software for comparative analyses of RNA pseudoknot structures, and, further, non-coding RNAs (cited from the original site). |
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| Data type | RNA |
Raccess
| Summary | Raccess is the tool for genome-scale computation of structural accessibility of RNA transcripts (cited from the original site). |
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| Data type | RNA |
RactIP
| Summary | RactIP can provide fast and accurate prediction of RNA-RNA interaction using integer programming. 4 tool archives (Source(version0.0.1 and 0.0.2), Windows, Linux) are ready. |
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| Data type | RNA RNA-RNA interaction |
Rchange
| Summary | Rchange compute energy changes of RNA secondary structures in response to base mutations(cited from original site). |
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| Data type | RNA |
Recount
| Summary | RECOUNT is a software for estimating the true count of Solexa readsbased on a probabilistic model. RECOUNT uses the quality score provided by Solexa and the reads as its input. Typical application of this software is for transcriptome or metagenomic expression analysis (cited from the original site). |
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| Data type | DNA-sequence Next Generation Sequencing Data |
Rentropy
| Summary | Rentropy computes entropy, mean energy, and variation of energy from the Boltzmann distribution of RNA secondary structures(cited from original site). |
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| Data type | RNA |
Rfold
| Summary | A base pair probability matrix that indicates the ease of secondary base energy pairing has often been used for sequence analysis of structural RNA. In recent years, it has been found that large amounts of non-protein-encoding RNAs are transcribed in higher eukaryotes, and in order to conduct sequence analysis of these RNAs, There is an increasing need for methods of determining local base pair probabilities where the distance is limited to W or less. In the past, there were only programs that used such probability calculations to use unrealistically simplified models and those that used approximate calculation methods. Rfold is the first software that can calculate local base pair probabilities without approximation based on the energy model of secondary structure. When the sequence length is N, Rfold calculates local base pair probability with the time complexity of O (NW2) and the complexity of O (N + W2) region. Furthermore, Rfold is implemented with an algorithm that predicts secondary structures based on the Maximal Expected Accuracy method, which has recently been validated. |
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| Data type | RNA |
RNAmine
| Summary | RNAmine is software for extracting stem patterns that frequently appear from RNA sequences using a graph mining. |
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| 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.suspending for relocation. (confirmation on 2012/11/05) |
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| Data type | Gene expression |