Publications - Published papers

Please find below publications of our group. Currently, we list 563 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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<tt>fragrep</tt>: Efficient Search for Fragmented Patterns in Genomic Sequences

Axel Mosig, Katrin Sameith, Peter F. Stadler


PREPRINT 04-019: [ PDF ]  [ PS ]  [ Software ]

Status: Published

Geno. Prot. Bioinfo. 4: 56-60 (2006).


Many classes of non-coding RNAs (including yRNAs, vaultRNAs, RNAse P and MRP RNA, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable length. Local alignment algorithms such as blast are therefore ill-suited for the discovery new homologs of such ncRNAs in genomic sequences. The fragrep tool instead implements an efficient algorithm for detecting pattern fragments that occur in a given order. For each pattern fragment a mismatches tolerance and bounds on the length of the intervening sequences can be specified separately.