In this way glbase acts as the 'glue' between up-stream analysis (e.g. the genomic alignment of sequencing reads and ChIP-seq peak discovery) and down-stream analysis (e.g. ChIP-seq peak annotation, combining ChIP-seq/RNA-seq data, and the production of publication-quality figures).
One of the powers of this approach is that the entire pipeline of methods used to assemble the correlation matrix is completely metadata independent – only the genomic alignment of probe sequences and the quantitative measurements made by the microarray were used.
We map the location of each vector feature, the bar code and the genomic alignment to the sequence using BioPerl graphics.
The first stage examines contig alignments to genomic sequences (contig-to-genome alignments) and identifies anomalous or non-reference (candidate) contigs that have a variety of alignment topologies.
The system uses the Grid computing paradigm [46] for the execution of computationally intensive steps involved in the TFBS finding process: genomic sequence alignment and TFBS searching.
Exons of PpTFL1 and PpAG were identified by alignment of genomic and cDNA sequences, and primer sets were developed that amplified exon regions.
We developed a genome-based computational pipeline that uses genomic alignments of mRNAs and probe set consensus sequences to identify high-quality probe sets and assign these to groups based on their patterns of genomic overlap.
It is noteworthy that due to the highly stringent mapping criteria applied in our previous studies [ 31, 32], a few mismatches in the alignments between the reference genomic sequence and the sequences generated from the Alu libraries were sufficient to lead to their classification as "partially mapped" reads.
Data types IGB can display include gene structure annotations, shown as linked blocks with taller blocks indicating translated regions; genomic alignments of expression array target sequences and probes, shown as linked blocks bearing smaller blocks representing probes; and EST/cDNA genomic alignments, shown as linked spans.
IY participated in genomic libraries analysis and sequence alignments.
To identify TEs which are likely to be new insertions in either mouse or rat, since these species diverged, we obtained RepeatMasker [31] annotation of TE sequences and genomic alignments from the UCSC Genome Browser [32] database for the mouse NCBI 36 (UCSC mm8) and the rat RGSC 3.4 (UCSC rn4) genome assemblies.
