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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) |
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| Data type | DNA, amino acid sequences |
Recount
| 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
| 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 |
seg-suite
| Summary | The seg suite provides tools for manipulating segments and alignments. It uses a format called "seg". This program converts segments or alignments from various formats to seg. |
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| Data type | DNA-sequence , RNA-sequence |
SlideSort
| 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 |
SNP-system
| Summary | We developed SNP-system which is unified in common interface and released it on the web.Website( http://www.h-invitational.jp/snps/ ) was closed, and at 22th Mar 2013, The archive opened in MEDALS Archive. |
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| Data type | DNA-sequence |
SPALN
| 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 |
tantan
| Summary | tantan is a tool to find cryptic repeats (low complexity and short-period tandem repeats) in DNA, RNA, and protein sequences.The aim of tantan is to prevent false predictions when searching for homologous regions between two sequences. You can get it from the archive page(cited from the original site). |
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| Data type | DNA-sequence , RNA, Aminoacid |
toxRank
| Summary | toxRnak is an application that displays a list of compounds with an expression profile similar to the expression pattern of the input gene group. Given a signature of query drug, toxRank computes the similarity with reference to expression profiles which are developed rank matrix data. It is possible to generate flexible rank matrix from genes that users consider important for hepatotoxicity and molecular panels obtained with toxBridge. |
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| Data type | - |
Web page checker
| 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 |
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