Use IGB to

View EST/cDNA alignment results

Next-generation sequencing technologies are making it much easier for individual labs to produce huge volumes of short- and long-read sequencing data. To get maximum value from these data, you often need to view the sequence reads alongside all the other known features in a genome. Using tools like blat and sim4, you can align your reads against the genome and then use IGB to view the alignments alongside canonical gene models provided by organizations such as The Arabidopsis Information Resource. IGB can read data in a variety of different formats, including: psl (from blat), bed (UCSC Genome Bioinformatics), and fasta (for sequence files).

View gene models and other annotations data

IGB can load data via the Internet using Web services (and from local files and directories). Currently, IGB accesses data provided by two different sites – our BioViz ArabiDAS site, which serves Arabidopsis data, and another site hosted by Affymetrix (NetAffx) which serves data from the human and many other genomes. Ultimately, we plan to support other plant genomes, as well. Data sites interested in hosting their own IGB-compatible data server sites should contact us for details.

Explore tiling array data

IGB can load data from tiling array results as genome graphs, which display probe intensity data alongside the genomic sequence. For information on how to do this, see the IGB user’s guide and the FAQ item on tiling arrays.