Tool catalog
Protein( 10/19 )
ALN
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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. |
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| Data type | DNA, amino acid sequences |
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 |
CoCoozo
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Summary | CoCoozo is a search engine for analyzing MS spectrum data. CoCoozo performs parallelized high-speed database search with a set of MS spectrum data against existing protein sequence databases in order to identify proteins corresponding to the precursor ions from peak intensity patterns. |
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| Data type | Ptotein-sequence |
DPClus
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Summary | DPClus is a graph clustering software, which makes it possible to detect and visualize clusters of proteins in interaction networks which mostly represent molecular biological functional units. |
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| Data type | Protein-function |
FORTE
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Summary | FORTE is a profile-profile comparison tool for protein fold recognition. Users can submit a protein sequence to explore the possibilities of structural similarity existing in known structures. Results are reported in the form of pairwise alignments. |
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| Data type | Protein-structure |
GPCRs Interaction Partners
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Summary | G-protein coupled receptor interaction partners (GRIP) is the web application to predict protein-protein interaction interfaces for G-protein coupled receptor oligomerization. This application provides predicted interfaces by Spatial Cluster Detection (SCD), Predicted interfaces are displayed interactively by using Jmol (cited from the original site). |
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| Data type | Interaction GPCR |
HEAT
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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 |
PAPIA
[ Official site (the link is in prep.) ]
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Summary | Tools for protein information analyses such as similar structure search, Homologous sequence search and Multiple sequence search by PC cluster. |
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| Data type | Protein-structure |
PMID-Extractor
None
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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. |
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| Data type | Journal |