PMID- 38110863
OWN - NLM
STAT- MEDLINE
DCOM- 20231220
LR  - 20240210
IS  - 1471-2105 (Electronic)
IS  - 1471-2105 (Linking)
VI  - 24
IP  - 1
DP  - 2023 Dec 18
TI  - PEPMatch: a tool to identify short peptide sequence matches in large sets of 
      proteins.
PG  - 485
LID - 10.1186/s12859-023-05606-4 [doi]
LID - 485
AB  - BACKGROUND: Numerous tools exist for biological sequence comparisons and search. 
      One case of particular interest for immunologists is finding matches for linear 
      peptide T cell epitopes, typically between 8 and 15 residues in length, in a 
      large set of protein sequences. Both to find exact matches or matches that 
      account for residue substitutions. The utility of such tools is critical in 
      applications ranging from identifying conservation across viral epitopes, 
      identifying putative epitope targets for allergens, and finding matches for 
      cancer-associated neoepitopes to examine the role of tolerance in tumor 
      recognition. RESULTS: We defined a set of benchmarks that reflect the different 
      practical applications of short peptide sequence matching. We evaluated a suite 
      of existing methods for speed and recall and developed a new tool, PEPMatch. The 
      tool uses a deterministic k-mer mapping algorithm that preprocesses proteomes 
      before searching, achieving a 50-fold increase in speed over methods such as the 
      Basic Local Alignment Search Tool (BLAST) without compromising recall. PEPMatch's 
      code and benchmark datasets are publicly available. CONCLUSIONS: PEPMatch offers 
      significant speed and recall advantages for peptide sequence matching. While it 
      is of immediate utility for immunologists, the developed benchmarking framework 
      also provides a standard against which future tools can be evaluated for 
      improvements. The tool is available at https://nextgen-tools.iedb.org , and the 
      source code can be found at https://github.com/IEDB/PEPMatch .
CI  - (c) 2023. The Author(s).
FAU - Marrama, Daniel
AU  - Marrama D
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Chronister, William D
AU  - Chronister WD
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Westernberg, Luise
AU  - Westernberg L
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Vita, Randi
AU  - Vita R
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Kosaloglu-Yalcin, Zeynep
AU  - Kosaloglu-Yalcin Z
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Sette, Alessandro
AU  - Sette A
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
AD  - University of California San Diego School of Medicine, La Jolla, San Diego, CA, 
      USA.
FAU - Nielsen, Morten
AU  - Nielsen M
AD  - Department of Health Technology, Technical University of Denmark, Lyngby, 
      Denmark.
FAU - Greenbaum, Jason A
AU  - Greenbaum JA
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA.
FAU - Peters, Bjoern
AU  - Peters B
AD  - Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, San 
      Diego, CA, USA. bpeters@lji.org.
AD  - University of California San Diego School of Medicine, La Jolla, San Diego, CA, 
      USA. bpeters@lji.org.
LA  - eng
GR  - U24 CA248138/CA/NCI NIH HHS/United States
GR  - U24CA248138/NH/NIH HHS/United States
PT  - Journal Article
DEP - 20231218
PL  - England
TA  - BMC Bioinformatics
JT  - BMC bioinformatics
JID - 100965194
RN  - 0 (Peptides)
RN  - 0 (Epitopes, T-Lymphocyte)
RN  - 0 (Proteome)
SB  - IM
MH  - Humans
MH  - Amino Acid Sequence
MH  - *Software
MH  - Peptides/chemistry
MH  - Algorithms
MH  - *Neoplasms
MH  - Epitopes, T-Lymphocyte
MH  - Proteome
PMC - PMC10726511
OTO - NOTNLM
OT  - BLAST comparison
OT  - Benchmarking
OT  - Immunology
OT  - K-mer mapping
OT  - Peptide matching
OT  - Sequence searching
OT  - T-cell epitopes
COIS- The authors declare no competing interests.
EDAT- 2023/12/19 06:42
MHDA- 2023/12/20 06:43
PMCR- 2023/12/18
CRDT- 2023/12/19 00:24
PHST- 2023/09/30 00:00 [received]
PHST- 2023/12/06 00:00 [accepted]
PHST- 2023/12/20 06:43 [medline]
PHST- 2023/12/19 06:42 [pubmed]
PHST- 2023/12/19 00:24 [entrez]
PHST- 2023/12/18 00:00 [pmc-release]
AID - 10.1186/s12859-023-05606-4 [pii]
AID - 5606 [pii]
AID - 10.1186/s12859-023-05606-4 [doi]
PST - epublish
SO  - BMC Bioinformatics. 2023 Dec 18;24(1):485. doi: 10.1186/s12859-023-05606-4.