Tool catalog
RNA( 10/31 )
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A Method for Extracting Optimal Sequence Related to Biological Activity
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Summary | This software can extract the optimal sequence relating to biological activity, if we have the data composed of sequences and corresponding activity, regardless of definition of characteristic sequence (cited from the original site). |
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| Data type | DNA-motif |
CentroidAlifold
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Summary | CentroidAlifold provides Accurate (common) secondary structure prediction for aligned RNA sequences. You can download CentroidAlifold software , which was contained in CentroidFold package (cited from the original site). |
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| Data type | RNA secondary structure |
CentroidAlign
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Summary | An accurate and fast aligner for multiple RNA sequences, based on maximizing the expected sum-of-pair score (SPS). You can get the archive file for linux and windows (cited from the original site). |
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| Data type | RNA alignment |
CentroidFold
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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. |
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| Data type | RNA |
CentroidHomfold
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Summary | CentroidHomfold provides RNA Secondary Structure prediction using Homologous Sequences. You can download CentroidHomfold software, which was contained in CentroidFold, or use CentroidHomfold-LAST Web-Server (cited from the original site). |
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| Data type | secondary structure |
HEAT
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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. |
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| Data type | Annotation |
IPknot
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Summary | RNA pseudoknot prediction based on maximizing expected accuracy (cited from the original site). |
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| Data type | RNA pseudoknot |
Idiographica
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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) |
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| Data type | Chromosome |
LAST
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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. |
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| Data type | DNA-sequence ,RNA, protein, user-defined alphabet. |
MAFFT
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Summary | MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. Download version (MacOS X, Windows, Linux, Source) and Online version is ready (cited from the original site). |
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| Data type | DNA-sequence alignment |
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