I have collection of specific breakpoints and their flanking sequences
I want to find out if their is something in common in between those sequences (trying to compare & find some similarity).
I am interested in any database to decipher sequence patterns, characteristics (motifs, repeats, physical characteristics etc.)
I have already tried :
MEME motif search;
Vienna package for secondary structures;
- Repeat masker;
- Blast2 - for similarity around the breakpoint;
- EMBOSS tools -UCSC tables for annotated info about repeats, histones, Dnase sites etc.
I am looking forward for any suggestions: TF binding, more secondary structures, more motifs, repeats and specific elements. Especialy protein (chromatin remodeling), nucleases , Ig target sites!
All suggestions are welcome - I am going to try them all.