ACT (Artemis Comparison Tool) can disply pairwise comparisons between two or more DNA sequences.
Looking for a method to get the upstream sequence (e.g. promoter) of a gene / TSS.
Because 454 reads often have unequal read lengths, I got an error using STAR. I got some success when using hisat2.
Notes on eukaryotic genome annotation.
An annotation transfer stratagy between different geome assemblies using RATT, Augustus, blast and scripting.
Mark Yandell & Daniel Ence. Nature Reviews Genetics 13, 329-342 (May 2012). doi:10.1038/nrg3174
- CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)
- Cas (CRISPR-associated genes)
- crRNA (CRISPR RNA)