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 |
LAMPLINK
| Summary | The LAMPLINK can detect statistically significant epistatic interactions of two or more SNPs from GWAS data. This software can be used in the same way as the widely used GWAS analysis software PLINK, but LAMPLINK has the additional options for the detection of epistatic interactions with LAMP, which is a multiple testing procedure for combinatorial effects discovery. |
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| Data type | DNA-sequnece |
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. |
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| Data type | DNA-sequence ,RNA, protein, user-defined alphabet. |
MAFFT
| 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 |
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| Data type | DNA-sequence alignment |
MDV
| Summary | Motif Distribution Viewer (MDV) is a web tool for visualizing the distribution of various motifs around transcription start sites (TSS) on a user-defined set of promoter sequences. The tool can be used on the original site, as well as downloaded to used locally. (cited from original site). |
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| Data type | DNA-motif |
NGSFeatGen
| Summary | This software is a framework for predicting true reads from the next generation sequencing data. This software generates several key features: observed count, estimate true count, loglikelihood with entropy penalty, loglikelihood ratio, expectation matching score, and specific correction coefficient. |
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| Data type | DNA-sequence NGS |
paraclu
| Summary | Paraclu finds clusters in data attached to sequences(cited from original site). |
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| Data type | DNA-sequence |
PHMMTS
| Summary | PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure (cited from the original site). |
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| 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, 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 |
Prediction program
| Summary | Gene prediction program can be deleted region search for the candidate region from the database, which does not contain essential genes or synthetic lethal gene, and alongside a series of adverse genetic traits such as the emergence of delayed growth and deletion mutations.(cited from the project reports) |
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| Data type | DNA-sequence |