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The alignment of protein superfamily sequences Part I: Identifying Cluster Specific Subsequences (CSS) in Protein Families
(A2B2C, 2015-10-14)
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances such as obtained by MAFFT and Promals3D, MSA construction of complex superfamilies remains problematic and requires ...
Cluster Specific Dunn index for co-expression detection
(A2B2C, 2015-10-14)
It is usually assumed that co-expressed genes suggest co-regulation in the underlying regulatory network. Determining sets of co-expressed genes is an important task, where significative groups of genes are defined based ...
The alignment of protein superfamily sequences Part II: Multiple Alignment Touch-up Engine (MATE)
(A2B2C, 2015-10-14)
Multiple Sequence Alignments (MSA) are crucial tools in protein bioinformatics. Despite recent advances, construction of MSAs for complex superfamilies remains problematic and requires rigorous manual correction. In this ...
Software and Protocol for Phenotype Classification based on SNPs
(A2B2C, 2011-05-10)
HMMer CTTer: Function assignation using HMMer profiles and reliable cut-offs
(A2B2C, 2011-05-10)