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Next-generation sequencing
- mrFAST:
Read mapper developed specifically for structural variation and
segmental duplication detection using the Illumina platform. Supports
small indel alignments.
- mrsFAST: Similar to mrFAST, Hamming
distance only.
- drFAST: Read mapper for di-base
color-space reads generated with the SOLiD platform.
- mrCaNaVaR: Read
depth analysis method to characterize segmental duplications and
predict absolute copy numbers.
- VariationHunter:
Structural variation calling algorithm using read pair mapping
information including suboptimal alignments.
- SPLITREAD: Detection
of structural variants and indels from genome and exome sequencing
data.
- NovelSeq: Novel
sequence insertion discovery framework.
- SCALCE: Tool to
efficiently compress FASTQ files.
RNA analysis
- taveRNA suite
- inteRNA: Algorithm
that predicts the joint secondary structure of two RNA sequences.
- alteRNA: Densityfold
algorithm that minimizes a
linear combination of energy density and the total free energy.
- pRuNA: RNA
interaction search engine. pRuNA is a sequence based pruning technique
that eliminates a significant fraction of a non coding RNA (ncRNA) data
set and retains only the most likely ncRNA candidates for forming a
stable joint structure with the query mRNA.
- piRNA: RNA-RNA
interaction partition function algorithm to predict the joint partition
function, equilibrium concentration, ensemble energy, and melting
temperature for two RNA sequences.
- smyRNA: Novel
ab initio non-coding RNA
finder.
Others
- MaM: A software
tool that processes and manipulates multiple alignments of genomic
sequences.
- RepeatNet: An ab initio centromeric sequence detection algorithm.