How to find the alignments

• Browsing: From the home page, click on a chromosome to see a list of matches sorted by cluster number or by genomic location. From the chromosome menu page you can choose lists of all matches, good matches and alternative splice candidates.
• Graphical chromosome display: This is also available for each chromosome as links from the home page. A vertical axis in the left frame represents the chromosome, with coordinates from the Golden Path chromosome sequences. Matches are displayed as bars to the right of the axis. Different colours are used for bad matches (blue), good matches (red), and alt. splice candidates (orange). Click on a match to display it. Click on the axis to zoom in. When the direction of a gene is known (inferred from splice signals), the match bar is equipped with an arrowhead (but only if there is room for it; one may have to zoom in to see it).
• Cluster search: If you are interested in a specific UniGene cluster, just type in the cluster name (e.g. "Hs635") in the search box on the home page, the chromosome menus, or the alignment displays. If there is more than one match, a list of matches sorted by quality is shown.
• Keyword or Blast search: You can use the GeneNest detailed query page to search the clusters by EST or gene accession number, clone id, clone library, or sequence annotation. You can also do a Blast search with a DNA or protein sequence.

The alignment display

Methods and presentation details

The chromosomes are the Apr 1, 2001 freeze of the HUGO Golden Path assembly [6] of the complete human genome.

Mapping and alignment

Before searching, repeat elements were filtered out using the program RepeatMasker by A.F.A. Smit and P. Green.

For each mathing cluster a refined search against the matching chromosome was made, in order to approximately determine a gene region containing all exons. In the refined search, all matches of length 30 with at most 2 errors were found.

Finally, for each cluster a spliced alignment of all contigs against the matching chromosome region(s) was determined using the program sim4 by Florea et al. [8] The exon positions, percentage identity and splice signals from this aligment are shown in the graphics.

The main criterion for including a match is that it contains a 100 bp region with at most 3 errors. Most such matches are aligned, but the following exceptional cases are skipped:

• Very short matches: matches whose total length (all exons) is less than 200 bp.
• Repeated matches: when a cluster has more than 20 mathces in a single chromosome, only the 20 best (according to the E-value from vmatch) are kept.

Automatic analysis and classification

When a cluster has more than one match, a table of all matches is shown when the cluster is searched. (When browsing matches, use the link containing the number of matches, just above the graphics, to display this table.) The matches are sorted by quality, starting with the best, according to the follwing criteria (by priority):

1. good matches before bad matches
2. highest number of exons
3. highest effective alignment length (#bp aligned in contig multiplied by % identity)

Only the good contigs are considered when detecting splice variants. If a match contains at least two good contigs, overlapping by at least 100 bp in the genomic sequence, the splice sites according to the alignments are compared and inconsistencies reported as possible splice variants. They are classified as missing exons, putative introns, or alternative donor/acceptor sites (must differ by at least 9 bp to be marked), or as combinations of these.

References

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