Home  Tool catalog

Genome / Gene( 10/20 )

Prev | Next | Display all results

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).
Data type DNA-motif

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.) ]
[ Show detail ]
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.

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 <∼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).
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).
Data type DNA-motif
Prev | Next | Display all results