PMID- 31068211
OWN - NLM
STAT- MEDLINE
DCOM- 20190523
LR  - 20200309
IS  - 1746-6148 (Electronic)
IS  - 1746-6148 (Linking)
VI  - 15
IP  - 1
DP  - 2019 May 8
TI  - Impact of alignment algorithm on the estimation of pairwise genetic similarity of 
      porcine reproductive and respiratory syndrome virus (PRRSV).
PG  - 135
LID - 10.1186/s12917-019-1890-0 [doi]
LID - 135
AB  - BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is a major 
      threat to the swine industry. It is caused by the PRRS virus (PRRSV). 
      Determination and comparison of the nucleotide sequences of PRRSV strains 
      provides useful information in support of control initiatives or epidemiological 
      studies on transmission patterns. The alignment of sequences is the first step in 
      analyzing sequence data, with multiple algorithms being available, but little is 
      known on the impact of this methodological choice. Here, a study was conducted to 
      evaluate the impact of different alignment algorithms on the resulting aligned 
      sequence dataset and on practical issues when applied to a large field database 
      of PRRSV open reading frame (ORF) 5 sequences collected in Quebec, Canada, from 
      2010 to 2014. Five multiple sequence alignment programs were compared: Clustal W, 
      Clustal Omega, Muscle, T-Coffee and MAFFT. RESULTS: The resulting alignments 
      showed very similar results in terms of average pairwise genetic similarity, 
      proportion of pairwise comparisons having >/=97.5% genetic similarity and sum of 
      pairs (SP) score, except for T-Coffee where increased length of aligned datasets 
      as well as limitation to handle large datasets were observed. CONCLUSIONS: Based 
      on efficiency at minimizing the number of gaps in different dataset sizes with 
      default open gap values as well as the capability to handle a large number of 
      sequences in a timely manner, the use of Clustal Omega might be recommended for 
      the management of PRRSV extensive database for both research and surveillance 
      purposes.
FAU - Lambert, Marie-Eve
AU  - Lambert ME
AUID- ORCID: 0000-0002-0109-3363
AD  - Laboratoire d'epidemiologie et de medecine porcine (LEMP), Faculty of Veterinary 
      Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada. 
      marie-eve.lambert@umontreal.ca.
AD  - Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of 
      Veterinary Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada. 
      marie-eve.lambert@umontreal.ca.
FAU - Arsenault, Julie
AU  - Arsenault J
AD  - Laboratoire d'epidemiologie et de medecine porcine (LEMP), Faculty of Veterinary 
      Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
AD  - Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of 
      Veterinary Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
FAU - Delisle, Benjamin
AU  - Delisle B
AD  - Laboratoire d'epidemiologie et de medecine porcine (LEMP), Faculty of Veterinary 
      Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
AD  - Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of 
      Veterinary Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
FAU - Audet, Pascal
AU  - Audet P
AD  - Laboratoire d'epidemiologie et de medecine porcine (LEMP), Faculty of Veterinary 
      Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
AD  - Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of 
      Veterinary Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
FAU - Poljak, Zvonimir
AU  - Poljak Z
AD  - Department of Population Medicine, Ontario Veterinary College, University of 
      Guelph, Guelph, Ontario, Canada.
FAU - D'Allaire, Sylvie
AU  - D'Allaire S
AD  - Laboratoire d'epidemiologie et de medecine porcine (LEMP), Faculty of Veterinary 
      Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
AD  - Swine and Poultry Infectious Diseases Research Center (CRIPA), Faculty of 
      Veterinary Medicine, Universite de Montreal, St. Hyacinthe, Quebec, Canada.
LA  - eng
GR  - Project #1343/Swine Cluster 2/
PT  - Journal Article
DEP - 20190508
PL  - England
TA  - BMC Vet Res
JT  - BMC veterinary research
JID - 101249759
SB  - IM
MH  - *Algorithms
MH  - *Genetic Variation
MH  - Porcine respiratory and reproductive syndrome virus/*genetics
MH  - Sequence Alignment/*methods/standards
PMC - PMC6505299
OTO - NOTNLM
OT  - Alignment algorithm
OT  - Genetic similarity
OT  - PRRS
OT  - Porcine reproductive and respiratory syndrome virus
OT  - Sequence
COIS- ETHICS APPROVAL AND CONSENT TO PARTICIPATE: Not applicable. CONSENT FOR 
      PUBLICATION: Not applicable. COMPETING INTERESTS: The authors declare that they 
      have no competing interests. PUBLISHER'S NOTE: Springer Nature remains neutral 
      with regard to jurisdictional claims in published maps and institutional 
      affiliations.
EDAT- 2019/05/10 06:00
MHDA- 2019/05/24 06:00
PMCR- 2019/05/08
CRDT- 2019/05/10 06:00
PHST- 2018/11/09 00:00 [received]
PHST- 2019/04/29 00:00 [accepted]
PHST- 2019/05/10 06:00 [entrez]
PHST- 2019/05/10 06:00 [pubmed]
PHST- 2019/05/24 06:00 [medline]
PHST- 2019/05/08 00:00 [pmc-release]
AID - 10.1186/s12917-019-1890-0 [pii]
AID - 1890 [pii]
AID - 10.1186/s12917-019-1890-0 [doi]
PST - epublish
SO  - BMC Vet Res. 2019 May 8;15(1):135. doi: 10.1186/s12917-019-1890-0.