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A Method for Extracting Optimal Sequence Related to Biological Activity
| 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
| 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
| 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
| 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
| 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 |
ChIP2LAMP
| Summary | Discovery of combinatorial regulations is a key to understand complex gene regulation machineries. Combining this scripts (chip2lamp) with a statistical analysis LAMP allows us to find statistically significant combinations by integrating ChIP-seqs and RNA-seqs. This can handle MACS1/2 result as a ChIP-seq peak caller and Cuffdiff result from RNA-seq. |
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| Data type | ChIP-sequence, RNA-sequence |
DAFS
| Summary | Simultaneous aligning and folding of RNA sequences by dual decomposition. DAFS can take FASTA formatted RNA sequences as input, then producea structural alignment. |
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| Data type | RNA |
Dnemulator
| Summary | DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion. |
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| Data type | DNA-sequence |
Fdur
| Summary | Fdur computes sufficient statistics of phylogenetic tree model(cited from original site). |
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| 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. |
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| Data type | Annotation |
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