Analysis Tools

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These tools have been developed by the research groups involved in Human Genome Center, and they are various tools for analyzing genome data. For specific questions about a tool, please contact the development group of the individual tool.

Neoantimon

Neoantimon is a package for searching for neo-antigens that are specific to cancer cells in the R environment (Mac/Linux). Input files such as text files generated by Genomon and VCF files generated by other mutation analysis programs can be used, and the binding affinity of the HLA molecules with mutated peptide fragments generated from single nucleotide variation (SNV), insertion and deletion (Indel), and structural variant (SV), can be calculated comprehensively. Neoantimon enables us to extract tumor specific peptides with high antigen-posting ability (neo-antigens).

EEM

Genomon maps a result file (FASTQ) sequencing the Exon region of the human genome to a reference genome (hg19), analyzes the data, and outputs a list of candidate mutations in TSV format that can be displayed in Excel.Genomon is a software pipeline that combines various open software such as BWA, GATK, Picard, Annovar, and cutadapt.

 
 
 
 
 
 
 
 
 
 
 

Genomon

Genomon-fusion is a pipeline that combines open software such as bowtie, blat, cap3, etc. Genomon-fusion extracts fusion genes from human whole transcriptome sequencing data and outputs a list of candidate genes in TSV format that can be displayed in Excel.

Open source clustering software

Genomon maps a result file (FASTQ) sequencing the Exon region of the human genome to a reference genome (hg19), analyzes the data, and outputs a list of candidate mutations in TSV format that can be displayed in Excel.Genomon is a software pipeline that combines various open software such as BWA, GATK, Picard, Annovar, and cutadapt.

SiGN-BN

SiGN-BN is software for estimating static/dynamic gene networks from gene expression data such as knockdown experiment data, individual tissue sample data, drug dose time series data, and so on. It can estimate various gene networks ranging from a small and precise gene networks to very large scale gene networks consisting of the whole human genes or probes. The estimated gene networks can also be analyzed by the Cell Illustrator Online.

SiGN-SSM

SiGN-SSM is software for estimating dynamic gene networks from short time, replicated, and irregular time interval expression data. It is suitable not only for analyzing temporal regulatory dependencies between genes, but also for the extraction of the differentially regulated genes from time series expression profiles. The estimated gene networks can also be analyzed by the Cell Illustrator Online. 

BioRuby

BioRuby is a bioinformatics library for the object oriented scripting language Ruby. The library contains useful methods for treating biological databases, sequence analysis softwares and web services to make daily tasks easier and to build automated pipelines of the analysis.

Cell Illustrator Online

Cell Illustrator Online (CIO) enables biologists to draw, model, elucidate and simulate complex biological processes and systems. In conjunction with its outstanding drawing capabilities, CIO allows researchers to model metabolic pathways, signal transduction cascades, gene regulatory pathways and dynamic interactions of various biological entities such as genomic DNA, mRNA and proteins. You can evaluate the Cell Illustrator Online for one month with registration. Cell Illustrator Online Player (viewer of CSML format) is available without registration. 

PSORT, PSORT II, iPSORT

A set of programs for the prediction of subcellular localization of proteis from its amino acid sequence and its origin (e.g., Gram-positive bacteria). Prof. Nakai (HGC) has been involved in all of their development.

Melina & Melina2

Melina is a user-friendly tool to help users to extract a set of common motifs shared by functionally-related DNA sequences. Namely, Melina enables users to compare the motif extraction results of a well-known program with a series of different parameter sets or to compare the results of different algorithms.

 

EGassembler

EGassembler is a web server, which provides an automated as well as a user-customized analysis tool for cleaning, repeat masking, vector trimming, organelle masking, clustering and assembling the of ESTs and genomic fragments.

TFBIND

Software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)) using the cut-offs originally estimated by Dr T. Tsunoda (SRC,RIKEN). His algorithm detected local over-representation of transcription factor binding sites and decided the optimum cut-off values for binding scores. Using the optimum cut-off values and transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, the prediction software finds transcription factor binding sites on genomic DNA with low false-negatives and low false-positives particularly for major binding sites besides others.

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