Software

Software

PATRONUS is a program designed to compute in a very fast way the exact probability of observing a given number of occurrences of a simple motif in a sequence.

Category:
Sequence Analysis

PATRONUS (from "PATtern Recognition by Optimized Numerical Universal Scoring") is a program designed to compute in a very fast way the exact probability of observing a given number of occurrences of a simple motif (that is, a continuous word without gaps) in a sequence. Its intended scope is the analysis of very long biological sequences, like chromosomes or whole genomes of complex organisms. The probability is computed on the basis of the Markovian statistics of order m for the sequence, that is the recorded number of the occurrences of all the submotifs of length m + 1 in the sequence. Contrary to what many people believe, computing such a probability for a generic motif is a computationally demanding task, mainly because motifs can overlap in non-trivial ways.

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PhylomeDB is a public database for complete collections of gene phylogenies (phylomes).

Category:
Gene Analysis

PhylomeDB is a public database for complete collections of gene phylogenies (phylomes). It allows users to interactively explore the evolutionary history of genes through the visualization of phylogenetic trees and multiple sequence alignments. Moreover, phylomeDB provides genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees.

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Website

The Plant Resistance Genes database (PRGdb; http://prgdb.org) is a comprehensive resource on resistance genes (R-genes), a major class of genes in plant genomes that convey disease resistance against pathogens.

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project is a program that projects genomic features onto their sequences.

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Application/Software

project is a program that projects genomic features onto their sequences. Please contact Sarah Djebali (sarah dot djebali at crg dot es for any question).

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Application/Software

Various R scripts for exploratory biological sequence-derived data analysis

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Webservice

SeAMotE (Sequence Analysis of Motifs Enrichment) allows fast and accurate large-scale de novo motif discovery in nucleic acid sequences.

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SECISaln will predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements.

Category:
Sequence Analysis
Type:
Webservice

SECISaln will predict a SECIS element in the query sequence, split it into its constituent parts and align these against a precompiled database of eukaryotic SECIS elements.

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In this web server we provide public access to two new computational methods for selenoprotein identification and analysis:

Type:
Webservice

In this web server we provide public access to two new computational methods for selenoprotein identification and analysis: SECISearch3 replaces its predecessor SECISearch as a tool for prediction of eukaryotic SECIS elements. Seblastian is a new method for selenoprotein gene detection that uses SECISearch3 and then predicts selenoprotein sequences encoded upstream of SECIS elements. Seblastian is able to both identify known selenoproteins and predict new selenoproteins. This project is the result of a collaboration with Vadim Gladyshev's lab in Harvard

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Selenoprofiles is a homology-based gene finding tool which is suitable for selenoprotein prediction in large nucleotide databases, like genomes.

Category:
Gene Analysis
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Application/Software

Selenoprofiles is a homology-based gene finding tool which is suitable for selenoprotein prediction in large nucleotide databases, like genomes. Selenoproteins are a group of proteins that contain selenocysteine (Sec), a rare amino acid inserted co-translationally into the protein chain. The Sec codon is UGA, which is normally a stop codon. In selenoproteins UGA is recoded to Sec in presence of specific signals on selenoprotein gene transcripts. Due to the dual role of the UGA codon, selenoprotein prediction and annotation are difficult tasks and are left mostly to manual analysis, since there are no reliable “golden standard” programs for this purpose. Here we present an homology-based in silico tool to scan genomes for members of the known selenoprotein families: selenoprofiles. This pipeline has features that make it suitable for selenoprotein prediction, and is shown to correctly predict selenoproteins that are badly annotated in Ensembl. Selenoprofiles is a python-built pipeline that internally runs psitblastn, exonerate, genewise and SECISearch.

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sgp2 is a program to predict genes by comparing anonymous genomic sequences from different species.

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Application/Software, Webservice

sgp2 is a program to predict genes by comparing anonymous genomic sequences from different species. It combines tblastx, a sequence similarity search program, with geneid, an ab initio gene prediction program.

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Application/Software

SJcount is a utility for fast SJ (splice-junction) quantification. It is an annotation-agnostic offset-aware version of bam2ssj

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SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell.

Category:
Systems Biology
Type:
Application/Software

SmartCell is a program developed to provide an idea of the evolution of a network in a whole, single cell. Based on stochastic algorithms, SmartCell needs multiple runs to have mean results. To help the user, SmartCell is distributed with a graphic user interface that allows for the creation of a model with a user friendly interface, as well as for the analysis and treatment of the results after the runs.

SmartCell is being developed by Luis Serrano and his team at the CRG in Barcelona.

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A database for the molecular phenotyping of human SNPs and disease mutations

Category:
Protein Function Analysis
Type:
Database

Single nucleotide polymorphisms (SNPs) are, together with copy number variation, the primary source of variation in the human genome. SNPs are associated with altered response to drug treatment, susceptibility to disease, and other phenotypic variation. Furthermore, during genetic screens for disease-associated mutations in groups of patients and control individuals, the distinction between disease causing mutations and polymorphisms is often unclear. Annotation of the functional and structural implications of single nucleotide changes thus provides valuable information to interpret and guide experiments.

SNPeffect is a database of non-synonymous SNPs and their predicted effect on the functional and physicochemical properties of the affected proteins. More precisely, SNPeffect analyses the effect of coding, non-synonymous SNPs on 3 categories of functional and physico-chemical properties of the affected proteins, namely protein structure and dynamics [stability, aggregation, dynamics, etc.], integrity of functional sites and cellular processing.

SNPeffect was originally developed by Joost Schymkowitz and Frederic Rousseau and their team at the SWITCH Laboratory of VIB in Brussels, Belgium, in collaboration with Luis Serrano and his team at the European Molecular Biology Laboratory in Heidelberg, Germany.

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Webservice

model Selection in Phylogenetics based on algebraic INvariants

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Application/Software

sQTLseekeR is a R package to detect splicing QTLs (sQTLs), which are variants associated with change in the splicing pattern of a gene. Here, splicing patterns are modeled by the relative expression of the transcripts of a gene.

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