Seq: A high-performance language for bioinformatics

Ariya Shajii, Ibrahim Numanagić, Riyadh Baghdadi, Bonnie Berger, Saman Amarasinghe

Research output: Contribution to journalArticlepeer-review

Abstract

The scope and scale of biological data are increasing at an exponential rate, as technologies like next-generation sequencing are becoming radically cheaper and more prevalent. Over the last two decades, the cost of sequencing a genome has dropped from $100 million to nearly $100Da factor of over 106Dand the amount of data to be analyzed has increased proportionally. Yet, as Moore's Law continues to slow, computational biologists can no longer rely on computing hardware to compensate for the ever-increasing size of biological datasets. In a field where many researchers are primarily focused on biological analysis over computational optimization, the unfortunate solution to this problem is often to simply buy larger and faster machines. Here, we introduce Seq, the first language tailored specifically to bioinformatics, which marries the ease and productivity of Python with C-like performance. Seq starts with a subset of PythonDand is in many cases a drop-in replacementDyet also incorporates novel bioinformatics- and computational genomics-oriented data types, language constructs and optimizations. Seq enables users to write high-level, Pythonic code without having to worry about low-level or domain-specific optimizations, and allows for the seamless expression of the algorithms, idioms and patterns found in many genomics or bioinformatics applications. We evaluated Seq on several standard computational genomics tasks like reverse complementation, k-mer manipulation, sequence pattern matching and large genomic index queries. On equivalent CPython code, Seq attains a performance improvement of up to two orders of magnitude, and a 160× improvement once domain-specific language features and optimizations are used. With parallelism, we demonstrate up to a 650× improvement. Compared to optimized C++ code, which is already difficult for most biologists to produce, Seq frequently attains up to a 2× improvement, and with shorter, cleaner code. Thus, Seq opens the door to an age of democratization of highly-optimized bioinformatics software.

Original languageEnglish (US)
Article numberA125
JournalProceedings of the ACM on Programming Languages
Volume3
Issue numberOOPSLA
DOIs
StatePublished - Oct 2019

Keywords

  • Bioinformatics
  • Computational biology
  • Domainspecific language
  • Optimization
  • Programming language
  • Python

ASJC Scopus subject areas

  • Software
  • Safety, Risk, Reliability and Quality

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