Analytics of Biological Sequence Data

Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule"

BACKGROUND:
Transmembrane helices (TMHs) frequently occur amongst protein architectures as means for proteins to attach to or embed into biological membranes. Physical constraints such as the membrane's hydrophobicity and electrostatic potential apply uniform requirements to TMHs and their flanking regions; consequently, they are mirrored in their sequence patterns (in addition to TMHs being a span of generally hydrophobic residues) on top of variations enforced by the specific protein's biological functions.

RESULTS:

type: 
Journal Paper
journal: 
BMC Biology 2017 Jul 24;15(1):66. doi: 10.1186/s12915-017-0404-4
pubmed: 
28738801
Url: 
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0404-4
Impact Factor: 
6.779
Date of acceptance: 
2017-08-07

xHMMER3x2: Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation

BACKGROUND:
While the local-mode HMMER3 is notable for its massive speed improvement, the slower glocal-mode HMMER2 is more exact for domain annotation by enforcing full domain-to-sequence alignments. Since a unit of domain necessarily implies a unit of function, local-mode HMMER3 alone remains insufficient for precise function annotation tasks. In addition, the incomparable E-values for the same domain model by different HMMER builds create difficulty when checking for domain annotation consistency on a large-scale basis.

RESULTS:

type: 
Journal Paper
journal: 
Biology Direct 2016, 11:63, DOI: 10.1186/s13062-016-0163-0
pubmed: 
27894340
Url: 
https://biologydirect.biomedcentral.com/articles/10.1186/s13062-016-0163-0
Impact Factor: 
3.016
Date of acceptance: 
2016-10-24

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Background: Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies.

type: 
Journal Paper
journal: 
Biology Direct (2015) 10:39, doi: 10.1186/s13062-015-0068-3
Impact Factor: 
4.66
Date of acceptance: 
2015-07-20
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