PPLine: An automated pipeline for SNP, SAP, and splice variant detection in the context of proteogenomics

Journal of Proteome Research

Volumn 14, Issue 9, 2015, Pages 3729-3737

  Krasnov, George Sergeevich ^a,b,c   Dmitriev, Alexey Alexandrovich ^a   Kudryavtseva, Anna Viktorovna ^a,d   Shargunov, Alexander Valerievich ^b,c   Karpov, Dmitry Sergeevich ^a,b   Uroshlev, Leonid Andreevich ^a   Melnikova, Natalya Vladimirovna ^a   Blinov, Vladimir Mikhailovich ^b,c   Poverennaya, Ekaterina Vladimirovna ^b   Archakov, Alexander Ivanovich ^b   Lisitsa, Andrey Valerievich ^b   Ponomarenko, Elena Alexandrovna ^b  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b INSTITUTE OF BIOMEDICAL CHEMISTRY   (Russian Federation)

^c MECHNIKOV RESEARCH INSTITUTE FOR VACCINES AND SERA   (Russian Federation)

^d P A Herzen Research Oncological Institute   (Russian Federation)

Author keywords

alternative reading frames; alternative splicing; C HPP; indel; proteotypic peptides; RNA seq; SAP; SNP

Indexed keywords

ACYLTRANSFERASE; CASPASE; HISTONE ACETYLTRANSFERASE GCN5; PEPTIDE; PROTEOTYPIC PEPTIDE; UNCLASSIFIED DRUG;

ALTERNATE READING FRAME; ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; GENE; GENETIC POLYMORPHISM; GENOMICS; HEPG2 CELL LINE; INDEL MUTATION; LIVER; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEOGENOMICS; PROTEOMICS; SINGLE AMINO ACID POLYMORPHISM; SINGLE NUCLEOTIDE POLYMORPHISM; SLMO1 GENE; TMEM8A GENE; AUTOMATION; HUMAN; TUMOR CELL LINE;

ALTERNATIVE SPLICING; AUTOMATION; CELL LINE, TUMOR; GENOMICS; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; PROTEOMICS;

EID: 84941129045     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b00490     Document Type: Article

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