PB1-F2 Finder: Scanning influenza sequences for PB1-F2 encoding RNA segments

David S. DeLuca, Derin B. Keskin, Guang Lan Zhang, Ellis L. Reinherz, Vladimir Brusic

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Background: PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of premature stop codons. This virulence factor is present in every influenza pandemic and major epidemic of the 20th century. Absence of PB1-F2 is associated with mild disease, such as the 2009 H1N1 ("swine flu"). Results: The analysis of 8608 segment 2 sequences showed that only 8.5% have been annotated for the presence of PB1-F2. Our analysis indicates that 75% of segment 2 sequences are likely to encode PB1-F2. Two major populations of PB1-F2 are of lengths 90 and 57 while minor populations include lengths 52, 63, 79, 81, 87, and 101. Additional possible populations include the lengths of 59, 69, 81, 95, and 106. Previously described sequences include only lengths 57, 87, and 90. We observed substantial variation in PB1-F2 sequences where certain variants show up to 35% difference to well-defined reference sequences. Therefore this dataset indicates that there are many more variants that need to be functionally characterized. Conclusions: Our web-accessible tool PB1-F2 Finder enables scanning of influenza sequences for potential PB1-F2 protein products. It provides an initial screen and annotation of PB1-F2 products. It is accessible at http://cvc.dfci. harvard.edu/pb1-f2.

Original languageEnglish
Title of host publication10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)
Volume12
EditionSUPPL. 13
Publication statusPublished - 2011
Externally publishedYes
Event10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Bioinformatics, InCoB 2011/ISCB-Asia 2011 - Kuala Lumpur, Malaysia
Duration: Nov 30 2011Dec 2 2011

Other

Other10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Bioinformatics, InCoB 2011/ISCB-Asia 2011
CountryMalaysia
CityKuala Lumpur
Period11/30/1112/2/11

Fingerprint

RNA
influenza
Human Influenza
Virulence Factors
Proteins
Scanning
Population
Reading Frames
virulence
Nonsense Codon
Pandemics
swine influenza
world wide web
stop codon
protein products
pandemic
Swine
proteins

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)
  • Artificial Intelligence
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Software

Cite this

DeLuca, D. S., Keskin, D. B., Zhang, G. L., Reinherz, E. L., & Brusic, V. (2011). PB1-F2 Finder: Scanning influenza sequences for PB1-F2 encoding RNA segments. In 10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet) (SUPPL. 13 ed., Vol. 12). [S6]

PB1-F2 Finder : Scanning influenza sequences for PB1-F2 encoding RNA segments. / DeLuca, David S.; Keskin, Derin B.; Zhang, Guang Lan; Reinherz, Ellis L.; Brusic, Vladimir.

10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). Vol. 12 SUPPL. 13. ed. 2011. S6.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

DeLuca, DS, Keskin, DB, Zhang, GL, Reinherz, EL & Brusic, V 2011, PB1-F2 Finder: Scanning influenza sequences for PB1-F2 encoding RNA segments. in 10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). SUPPL. 13 edn, vol. 12, S6, 10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Bioinformatics, InCoB 2011/ISCB-Asia 2011, Kuala Lumpur, Malaysia, 11/30/11.
DeLuca DS, Keskin DB, Zhang GL, Reinherz EL, Brusic V. PB1-F2 Finder: Scanning influenza sequences for PB1-F2 encoding RNA segments. In 10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). SUPPL. 13 ed. Vol. 12. 2011. S6
DeLuca, David S. ; Keskin, Derin B. ; Zhang, Guang Lan ; Reinherz, Ellis L. ; Brusic, Vladimir. / PB1-F2 Finder : Scanning influenza sequences for PB1-F2 encoding RNA segments. 10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet). Vol. 12 SUPPL. 13. ed. 2011.
@inproceedings{14f404eb22724ed4b5c7ed5ab04588dc,
title = "PB1-F2 Finder: Scanning influenza sequences for PB1-F2 encoding RNA segments",
abstract = "Background: PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of premature stop codons. This virulence factor is present in every influenza pandemic and major epidemic of the 20th century. Absence of PB1-F2 is associated with mild disease, such as the 2009 H1N1 ({"}swine flu{"}). Results: The analysis of 8608 segment 2 sequences showed that only 8.5{\%} have been annotated for the presence of PB1-F2. Our analysis indicates that 75{\%} of segment 2 sequences are likely to encode PB1-F2. Two major populations of PB1-F2 are of lengths 90 and 57 while minor populations include lengths 52, 63, 79, 81, 87, and 101. Additional possible populations include the lengths of 59, 69, 81, 95, and 106. Previously described sequences include only lengths 57, 87, and 90. We observed substantial variation in PB1-F2 sequences where certain variants show up to 35{\%} difference to well-defined reference sequences. Therefore this dataset indicates that there are many more variants that need to be functionally characterized. Conclusions: Our web-accessible tool PB1-F2 Finder enables scanning of influenza sequences for potential PB1-F2 protein products. It provides an initial screen and annotation of PB1-F2 products. It is accessible at http://cvc.dfci. harvard.edu/pb1-f2.",
author = "DeLuca, {David S.} and Keskin, {Derin B.} and Zhang, {Guang Lan} and Reinherz, {Ellis L.} and Vladimir Brusic",
year = "2011",
language = "English",
volume = "12",
booktitle = "10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)",
edition = "SUPPL. 13",

}

TY - GEN

T1 - PB1-F2 Finder

T2 - Scanning influenza sequences for PB1-F2 encoding RNA segments

AU - DeLuca, David S.

AU - Keskin, Derin B.

AU - Zhang, Guang Lan

AU - Reinherz, Ellis L.

AU - Brusic, Vladimir

PY - 2011

Y1 - 2011

N2 - Background: PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of premature stop codons. This virulence factor is present in every influenza pandemic and major epidemic of the 20th century. Absence of PB1-F2 is associated with mild disease, such as the 2009 H1N1 ("swine flu"). Results: The analysis of 8608 segment 2 sequences showed that only 8.5% have been annotated for the presence of PB1-F2. Our analysis indicates that 75% of segment 2 sequences are likely to encode PB1-F2. Two major populations of PB1-F2 are of lengths 90 and 57 while minor populations include lengths 52, 63, 79, 81, 87, and 101. Additional possible populations include the lengths of 59, 69, 81, 95, and 106. Previously described sequences include only lengths 57, 87, and 90. We observed substantial variation in PB1-F2 sequences where certain variants show up to 35% difference to well-defined reference sequences. Therefore this dataset indicates that there are many more variants that need to be functionally characterized. Conclusions: Our web-accessible tool PB1-F2 Finder enables scanning of influenza sequences for potential PB1-F2 protein products. It provides an initial screen and annotation of PB1-F2 products. It is accessible at http://cvc.dfci. harvard.edu/pb1-f2.

AB - Background: PB1-F2 is a major virulence factor of influenza A. This protein is a product of an alternative reading frame in the PB1-encoding RNA segment 2. Its presence of is dictated by the presence or absence of premature stop codons. This virulence factor is present in every influenza pandemic and major epidemic of the 20th century. Absence of PB1-F2 is associated with mild disease, such as the 2009 H1N1 ("swine flu"). Results: The analysis of 8608 segment 2 sequences showed that only 8.5% have been annotated for the presence of PB1-F2. Our analysis indicates that 75% of segment 2 sequences are likely to encode PB1-F2. Two major populations of PB1-F2 are of lengths 90 and 57 while minor populations include lengths 52, 63, 79, 81, 87, and 101. Additional possible populations include the lengths of 59, 69, 81, 95, and 106. Previously described sequences include only lengths 57, 87, and 90. We observed substantial variation in PB1-F2 sequences where certain variants show up to 35% difference to well-defined reference sequences. Therefore this dataset indicates that there are many more variants that need to be functionally characterized. Conclusions: Our web-accessible tool PB1-F2 Finder enables scanning of influenza sequences for potential PB1-F2 protein products. It provides an initial screen and annotation of PB1-F2 products. It is accessible at http://cvc.dfci. harvard.edu/pb1-f2.

UR - http://www.scopus.com/inward/record.url?scp=84871910429&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84871910429&partnerID=8YFLogxK

M3 - Conference contribution

VL - 12

BT - 10th International Conference on Bioinformatics - 1st ISCB Asia Joint Conference 2011, InCoB 2011/ISCB-Asia 2011: Bioinformatics - Proceedings from Asia Pacific Bioinformatics Network (APBioNet)

ER -