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Genome / Gene( 10/13 )

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ALN

Summary Aln is a program for aligning a pair of nucleotide or amino acid sequences or alignments. Aln can even align a nucleotide sequence and a single or a group of protein sequences. This can be used to predict eukaryotic gene structures (protein-coding exons) based on sequence homology with known protein sequences.
Data type DNA, amino acid sequences

ALNGG

Summary ALNGG detects the protein coding gene by genome comparison between two species.
Data type DNA-sequence , Genome

ASIAN

Summary ASIAN is a tool for automatically inferring the relationships between objects from data including redundant information, e.g. expression profiles that were measured for a large number of genes under various conditions. The tool combines cluster analysis, regression analysis, and graphical Gaussian modeling. By inputting your raw data, you can obtain some relationships between objects: the correlation, the grouping, the group number, and the network graph.
Data type Gene expression profile

GUPPY

Summary GUPPY is a program to visualize sequence annotation data of the genetic sequence data with graphical layout.
Data type DNA-sequence

GeneDecoder

[ Official site (the link is in prep.) ]
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Summary GeneDecoder is a gene finding technology for eukaryotes, based on hidden Markov models (HMMs). The algorithm, using dynamic programing method and statistic models trained by annotated genome sequences, divides the input nucleic acid sequence into some meaningful segments.
Data type DNA-sequence , Eukaryote gene

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

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.

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).
Data type DNA-motif

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

PRRN

Summary PRRN is a multiple sequence alignment program by doubly nested randomized iterative method. PRRN accepts either nucleotide or protein sequences. PRRN repeatedly uses pairwise group-to-group alignment to improve the overall weighted sum-of-pairs score at each iterative step, where the pair weights are introduced to correct for uneven representations of the sequences to be aligned. The strategies of PRRN work most effectively for refining a crude alignment obtained by other more rapid methods, e.g. progressive alignment. (Summarized from the original site)
Data type DNA, amino acid sequences
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