Sentence examples for degenerate patterns from inspiring English sources

If we consider now degenerate patterns instead of simple words (see table 5), FMCI approach clearly outperforms the SR one.

When searching for degenerate patterns, putative calcium binding regions were consistently found (data not shown) but no positional conservation of these putative sites in multiple alignment was observed.

Scanning of canonical PROSITE motifs and signatures was performed using the ScanProsite tool [ 49] available at the ExPAsy server http://www.expasy.org, whereas scanning for degenerate patterns was performed using PROSITE scan available on-line at the IBCP-PBIL server http://npsa-pbil.ibcp.fr and allowing for 2 mismatches or setting for 65% similarity.

However, wide-spread DNA losses following replication events often lead to a degenerate pattern of correspondence.

When a degenerate pattern (finite set of words) is considered instead of a single word, it is easy to adapt this method by summing the contribution p of each word belonging to the pattern.

The program interface admits special formats to describe probability models of various types (HMM, Bernoulli, Markov); a pattern can be described with a list of words, a PSSM, a degenerate pattern or a word and a number of mismatches.

For a degenerate pattern of length h, L is more difficult to know as it depends on the degeneracy of the patterns, in the worst case L = k h -1, but L should be far smaller in most cases.

In order to count overlapping occurrences of a non degenerate pattern of length h on a size k alphabet we get L = k + h - 2 when an order 1 Markov model is considered and L = k m + h - m - 1 for an order m > 1 Markov model.

In principle, since the set of non-degenerate patterns forms a basis of the "snapshots space", any arbitrary spatial pattern might be possible at any given time during the spontaneous activity.

Nevertheless, as considering degenerated patterns roughly multiply their observed number of occurrences by the alphabet size for each inde-termination, the corresponding computational time grows in the same manner which usually limits the use of high degenerated patterns in practical cases.

If no SECISes are found matching this pattern, SECISearch is run with two increasingly degenerate SECIS patterns (all patterns are reported in Supplementary Material, Section S1).