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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). |
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| 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. |
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| Data type | DNA, amino acid sequences |
ALNGG
| Summary | ALNGG detects the protein coding gene by genome comparison between two species. |
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| 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. |
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| Data type | Gene expression profile |
ChIP2LAMP
| Summary | Discovery of combinatorial regulations is a key to understand complex gene regulation machineries. Combining this scripts (chip2lamp) with a statistical analysis LAMP allows us to find statistically significant combinations by integrating ChIP-seqs and RNA-seqs. This can handle MACS1/2 result as a ChIP-seq peak caller and Cuffdiff result from RNA-seq. |
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| Data type | ChIP-sequence, RNA-sequence |
COSMOS
| 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 |
Dnemulator
| Summary | DNemulator is a package for simulating DNA sequencing errors, polymorphisms, cytosine methylation and bisulfite conversion. |
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| Data type | DNA-sequence |
fastapl
| 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 |
GeneDecoder
| 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 |
GUPPY
| 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 |
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