Bioinformatics

Basic Services

Andalusian Platform of Bioinformatics (PAB) provides users multiple virtual machines with bioinformatic software installed. Users have instant access to a range of  graphical software applications  (with desktop interface), documentation and all bioinformatics packages  including sequence alignment, clustering, assembly, display, editing, and phylogeny also gene expression analysis and functinal analysis tools. Each tool’s functionality is fully described in the documentation directly accessible from the graphical interface of the virtual machine. See here for a complete list.

 It´s recommended not to exceed of ~10 millions of reads.

*OmicsOffice Suite of Integromics

De novo genome assembly

De novo genome assembly is a difficult process that must be adapted to each assembly project. We are able to design the appropriate assembly strategy for your project. We will assemble, analyze and deliver a finished genome, or part of a genome, along with customized visualizations and reports. We are highly experienced in working with data generated from Roche 454, Illumina, ABI SOLiD, and Sanger sequencing platforms. 

Transcriptome assembly

Adjusting the de novo assembly strategy  depend of organism´s complexity and it is the preferred method to find genes expressed in a non-model organism (with unknown genome). Our assembly tools reliably provide a detailled overview of all expressed genes in the species of interest. We are able to assembly long read (sanger and 454) or short reads (Solid, Illumina) using software tools like MIRA/SOAP /Oasis to give the best transcriptome.

RNA-seq data analysis

Quantification using RNA-Seq is used to analyze gene expression  under specific conditions, this method provides greater sensitivity and reproducibility than the threshold of the given microarrays. We are able to analyse gene expressions using next-gen sequencer Illumina HiSeq 2000/2500 and provides differential gene expression.

Microarray data analysis

We can analyse gene expression profiling data for all the major commercial microarray (Affymetrix, Illumina, Agilent) as well custom microarray platforms. We offer a wide range of statistical and bioinformatic analyses of microarray data, ranging from basic quality control and differential gene expression analysis to functional analysis.

Custom tools development

Custom made bioinformatics solutions for you.

The aim of any research project is is to obtain as much information as possible with the data that is available. Choose the better technology (or combination of two o more technologies) is very important, however choose the bioinformatics approaches is important too. There are many questions, such as:

Which of the software tools available are able to process and analyze the volumes of data?
How can one rate the quality of the analysis?
Does it make sense to store raw data for future research?

We can help you with the answers.