Frequently Asked Questions
Q: How should I interpret the alignment plots?
A: Pink lines connect identical bases where both bases are exonic in human and mouse. Blue lines connect identical bases in all other cases.
Q: What do the different evolutionary metrics mean?
- Transcript-genome identity refers to the percent of basepairs across the mouse lncRNA loci (exons and introns) that can be aligned and is identical to the human lncRNA loci.
- Transcript-transcript identity is the percent of of bases from the mouse lncRNA exons that can be aligned and is identical to a a human lncRNA exonic base pair.
- Splice site conservation is the number of splice sites that are conserved. (Acceptor and donor sites each count as 0.5.)
- Indel rate is the log2 ratio of the percent of indels found in exons compared to the percent of indels found in introns.
For more detailed explanation, please refer to our paper
Q: What would a coding gene look like?
A: As you might expect, coding genes align extremely well with high transcript-transcript identy and transcript-genome identity and almost always have every splice site conserved. The indel rate is low, with much less indels at exons than at introns. Here is how coding gene ACTB
would look with our alignments and metrics.
The slncky Evolution Browser
was developed as a collaboration between the Garber Lab
at UMass Medical and the Regev Lab at the Broad Institute.