PMID- 8435775
OWN - NLM
STAT- MEDLINE
DCOM- 19930322
LR  - 20191023
IS  - 0266-7061 (Print)
IS  - 0266-7061 (Linking)
VI  - 9
IP  - 1
DP  - 1993 Feb
TI  - An algorithm for the identification of similar oligopeptides between amino acid 
      sequences.
PG  - 93-100
AB  - Molecular mimicry is the origin of common structural patterns in sequences of 
      viral and host proteins, and it appears to be related to the development of 
      autoimmune diseases. The identification of structural molecular similarities 
      among viral and host proteins is thus very relevant in the development of 
      engineered antiviral vaccines to avoid potentially dangerous effects. In this 
      respect identifying pairs of similar oligopeptides between given proteins, 
      independently of the overall degree of similarity of their amino acid sequences, 
      is of interest. To this aim we have designed and implemented an algorithm capable 
      of finding and classifying (with respect to their statistical significance) all 
      possible pairs of similar oligopeptides between two proteins irrespective of 
      length, number, location and ordering of the pairs along the sequences. The 
      algorithm is very efficient and much more suited for this kind of local search 
      than standard alignment programs. The latter, dealing with the sequences as a 
      whole, are, in these cases, of very limited applicability. We have used the 
      algorithm to compare a glycoprotein of the human immunodeficiency virus (HIV) 
      type 1 and with the beta-chains of human leukocyte antigen (HLA). Besides a 
      previously identified peptide, we have found a new peptide located in the fusion 
      site of HIV that shares high similarity with the transmembrane domains of HLA.
FAU - Balzarotti, V
AU  - Balzarotti V
AD  - Department of Physics, University of Rome Tor Vergata, Italy.
FAU - Colizzi, V
AU  - Colizzi V
FAU - Morante, S
AU  - Morante S
FAU - Parisi, V
AU  - Parisi V
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - England
TA  - Comput Appl Biosci
JT  - Computer applications in the biosciences : CABIOS
JID - 8511758
RN  - 0 (HIV Envelope Protein gp120)
RN  - 0 (HIV Envelope Protein gp41)
RN  - 0 (Histocompatibility Antigens Class II)
RN  - 0 (Oligopeptides)
SB  - IM
MH  - *Algorithms
MH  - Amino Acid Sequence
MH  - HIV Envelope Protein gp120/chemistry
MH  - HIV Envelope Protein gp41/chemistry
MH  - Histocompatibility Antigens Class II/chemistry
MH  - Molecular Sequence Data
MH  - Oligopeptides/*chemistry
MH  - Programming Languages
MH  - Software
EDAT- 1993/02/01 00:00
MHDA- 1993/02/01 00:01
CRDT- 1993/02/01 00:00
PHST- 1993/02/01 00:00 [pubmed]
PHST- 1993/02/01 00:01 [medline]
PHST- 1993/02/01 00:00 [entrez]
AID - 10.1093/bioinformatics/9.1.93 [doi]
PST - ppublish
SO  - Comput Appl Biosci. 1993 Feb;9(1):93-100. doi: 10.1093/bioinformatics/9.1.93.