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Tool catalog

DNA, Genome ( 30 )
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 |
ALN
ALNGG
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Summary | ALNGG detects the protein coding gene by genome comparison between two species. |
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Data type | "DNA-sequence , Genome" |
ASIAN
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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. " |
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Data type | Gene expression profile |
COSMOS
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Summary | "COSMOS can detect somatic structural variations from whole genome short-read sequences. Also, it can be applicable to de novo SV detection in a family trio" |
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Data type | DNA-sequnece |
ChIP2LAMP
Dnemulator
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Summary | "DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion." |
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Data type | DNA-sequence |
GUPPY
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Summary | GUPPY is a program to visualize sequence annotation data of the genetic sequence data with graphical layout. |
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Data type | DNA-sequence |
GeneDecoder
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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." |
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Data type | "DNA-sequence , Eukaryote gene" |
HEAT
LAMPLINK
LAST
MAFFT
MDV
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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
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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 |
PHMMTS
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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
PRRN
Prediction program
Recount
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Summary | RECOUNT is a software for estimating the true count of Solexa readsbased on a probabilistic model. RECOUNT uses the quality score provided by Solexa and the reads as its input. Typical application of this software is for transcriptome or metagenomic expression analysis (cited from the original site). |
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Data type | DNA-sequence Next Generation Sequencing Data |
SCARNA Local Multiple
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Summary | "SCARNA_LM (SCARNA Local Multiple) is a local multiple aligner for RNA sequences. It is based on a discriminative pairwise alignment model which incorporates secondary structure features as base pairing probability calculrated by Rfold, and uses an efficient local multiple alignment construction procedure proposed by Phuong et al for local multiple alignment of protein sequences (cited from the original site). " |
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Data type | RNA alignment |
SNP-system
SPALN
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Summary | Spaln is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. |
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Data type | Comparative genomics |
SlideSort
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Summary | SlideSort is fast and exact method that can find all similar pairs from a string pool in terms of edit distance (cited from the original site). |
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Data type | DNA-sequence Protein-sequence |
Web page checker
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Summary | "A web page checker. This tool can monitor web pages, and grouping of web pages, highlight changes in a page, and send Email reports. " |
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Data type | Web contents |
fastapl
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Summary | "FASTA Perl Loop, a tool for processing multifasta data. Pronounced as ""fast apple"". and its companion program fastqpl, pronounced ""fast Q-ple"", for fastq format data. " |
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Data type | DNA-sequence |
paraclu
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Summary | Paraclu finds clusters in data attached to sequences(cited from original site). |
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Data type | DNA-sequence |