PMID- 20013221
OWN - NLM
STAT- MEDLINE
DCOM- 20100222
LR  - 20091216
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 615
DP  - 2010
TI  - Bioinformatic identification of plant peptides.
PG  - 375-83
LID - 10.1007/978-1-60761-535-4_26 [doi]
AB  - Plant peptides play a number of important roles in defence, development and many 
      other aspects of plant physiology. Identifying additional peptide sequences 
      provides the starting point to investigate their function using molecular, 
      genetic or biochemical techniques. Due to their small size, identifying peptide 
      sequences may not succeed using the default bioinformatic approaches that work 
      well for average-sized proteins. There are two general scenarios related to 
      bioinformatic identification of peptides to be discussed in this paper. In the 
      first scenario, one already has the sequence of a plant peptide and is trying to 
      find more plant peptides with some sequence similarity to the starting peptide. 
      To do this, the Basic Local Alignment Search Tool (BLAST) is employed, with the 
      parameters adjusted to be more favourable for identifying potential peptide 
      matches. A second scenario involves trying to identify plant peptides without 
      using sequence similarity searches to known plant peptides. In this approach, 
      features such as protein size and the presence of a cleavable amino-terminal 
      signal peptide are used to screen annotated proteins. A variation of this method 
      can be used to screen for unannotated peptides from genomic sequences. 
      Bioinformatic resources related to Arabidopsis thaliana will be used to 
      illustrate these approaches.
FAU - Lease, Kevin A
AU  - Lease KA
AD  - Division of Biological Sciences and Bond Life Sciences Centre, University of 
      Missouri, Columbia, MO, USA.
FAU - Walker, John C
AU  - Walker JC
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Arabidopsis Proteins)
RN  - 0 (Peptides)
SB  - IM
MH  - Amino Acid Sequence
MH  - *Arabidopsis/chemistry/genetics
MH  - Arabidopsis Proteins/chemistry/*genetics
MH  - Computational Biology/*methods
MH  - Databases, Protein
MH  - Molecular Sequence Data
MH  - Peptides/chemistry/*genetics
MH  - Sequence Analysis, Protein
MH  - Sequence Homology, Amino Acid
EDAT- 2009/12/17 06:00
MHDA- 2010/02/23 06:00
CRDT- 2009/12/17 06:00
PHST- 2009/12/17 06:00 [entrez]
PHST- 2009/12/17 06:00 [pubmed]
PHST- 2010/02/23 06:00 [medline]
AID - 10.1007/978-1-60761-535-4_26 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2010;615:375-83. doi: 10.1007/978-1-60761-535-4_26.