BOL

www.biostat.wisc.edu - Our basic strategy in building homology maps is to use exons that are orthologous in multiple genomes as map "anchors." Given K genomes, the steps in the map construction are as follows: For each genome, obtain a set of exon annotations. These...

As part of the PhD program in Computer Science at University of Essex, I am looking for a PhD student in computational and synthetic biology. The ideal candidate is interested in designing new biological design automation methods for genome scale...

github.com - maftools - An R package to summarize, analyze and visualize MAF files. Introduction. With advances in Cancer Genomics, Mutation Annotation Format (MAF) is being widley accepted and used to store variants detected. The Cancer Genome Atlas Project...

genometools.org - The AnnotationSketch module is a versatile and efficient C-based drawing library for GFF3-compatible genomic annotations. It is included in the GenomeTools distribution. Additionally, bindings to...

dunbrack.fccc.edu - BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers: optimized to work with vast amount of data...

www.biostars.org - MAKER is a great tool for annotating a reference genome using empirical and ab initiogene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite...

dagchainer.sourceforge.net - The DAGchainer software computes chains of syntenic genes found within complete genome sequences. As input, DAGchainer accepts a list of gene pairs with sequence homology along with their genome coordinates. Using a scoring function which accounts...

github.com - ConPADE (Contig Ploidy and Allele Dosage Estimation), a probabilistic method that estimates the ploidy of any given contig/scaffold based on its allele proportions. In the process, they report findings regarding errors in sequencing. The method can...

sourceforge.net - PBJelly - the genome upgrading tool. PBHoney - the structural variation discovery tool Both are contained within the PBSuite code found in downloads.----- PBJelly -----Read The...

github.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...