You are here

Home

Linux/Unix

CluePedia

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

The CluePedia Cytoscape plugin is a search tool for new markers potentially associated to pathways. CluePedia calculates linear and non-linear statistical dependencies from experimental data. Genes, proteins and miRNAs can be connected based on in silico and/or experimental information and integrated into a ClueGO network of terms/pathways. Interrelations within each pathway can be investigated, and new potential associations may be revealed through gene/protein/miRNA enrichments. A pathway-like visualization can be created using the Cerebral plugin layout.

Rating: 
Average: 5 (1 vote)

BayesMiRNAfind

Submitted by ChenLiang on Tue, 01/09/2018 - 17:36

Most computational methodologies for microRNA gene prediction utilize techniques based on sequence conservation and/or structural similarity. In this study we describe a new technique, which is applicable across several species, for predicting miRNA genes. This technique is based on machine learning, using the Naive Bayes classifier. It automatically generates a model from the training data, which consists of sequence and structure information of known miRNAs from a variety of species.

Rating: 
Average: 5 (1 vote)

microPred

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

In this article, we show that the classification of human precursor microRNA (pre-miRNAs) hairpins from both genome pseudo hairpins and other non-coding RNAs (ncRNAs) is a common and essential requirement for both comparative and non-comparative computational recognition of human miRNA genes. However, the existing computational methods do not address this issue completely or successfully. Here we present the development of an effective classifier system (named as microPred) for this classification problem by using appropriate machine learning techniques.

Rating: 
Average: 5 (1 vote)

segemehl

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions. Current evaluations indicate, however, that very different error models apply to the novel high-throughput sequencing methods. While the most frequent error-type in Illumina reads are mismatches, reads produced by 454's GS FLX predominantly contain insertions and deletions (indels).

Rating: 
5
Average: 5 (2 votes)

CORNA

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

With the increasing use of post-genomics techniques to examine a wide variety of biological systems in laboratories throughout the world, scientists are often presented with lists of genes that they must make sense of. A consistently challenging problem is that of defining co-regulated genes within those gene lists. In recent years, microRNAs have emerged as a mechanism for regulating several cellular processes.

Rating: 
Average: 5 (1 vote)

SNMNMF

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

It is well known that microRNAs (miRNAs) and genes work cooperatively to form the key part of gene regulatory networks. However, the specific functional roles of most miRNAs and their combinatorial effects in cellular processes are still unclear. The availability of multiple types of functional genomic data provides unprecedented opportunities to study the miRNA-gene regulation. A major challenge is how to integrate the diverse genomic data to identify the regulatory modules of miRNAs and genes.

Rating: 
Average: 5 (1 vote)

miRDeep*

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

miRDeep and its varieties are widely used to quantify known and novel micro RNA (miRNA) from small RNA sequencing (RNAseq). This article describes miRDeep*, our integrated miRNA identification tool, which is modeled off miRDeep, but the precision of detecting novel miRNAs is improved by introducing new strategies to identify precursor miRNAs. miRDeep* has a user-friendly graphic interface and accepts raw data in FastQ and Sequence Alignment Map (SAM) or the binary equivalent (BAM) format.

Rating: 
Average: 5 (1 vote)

Empirical GO

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

Many studies have investigated the differential expression of microRNAs (miRNAs) in disease states and between different treatments, tissues and developmental stages. Given a list of perturbed miRNAs, it is common to predict the shared pathways on which they act. The standard test for functional enrichment typically yields dozens of significantly enriched functional categories, many of which appear frequently in the analysis of apparently unrelated diseases and conditions.

Rating: 
Average: 5 (1 vote)

RNAither

Submitted by ChenLiang on Fri, 09/02/2016 - 21:59

We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for data normalization, different statistical tests for the identification of significant siRNAs, and a significance analysis of the biological processes involving corresponding genes.

Rating: 
Average: 5 (1 vote)

PatMaN

Submitted by ChenLiang on Sun, 09/10/2017 - 20:06

We present a tool suited for searching for many short nucleotide sequences in large databases, allowing for a predefined number of gaps and mismatches. The commandline-driven program implements a non-deterministic automata matching algorithm on a keyword tree of the search strings. Both queries with and without ambiguity codes can be searched. Search time is short for perfect matches, and retrieval time rises exponentially with the number of edits allowed.

Rating: 
Average: 5 (1 vote)

Pages

Subscribe to Linux/Unix