Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing

Juan González-Vallinas; Sonja Althammer; Eduardo Eyras

doi:10.1007/978-3-642-28062-7_9

Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing

Juan González-Vallinas^*, Sonja Althammer, Eduardo Eyras

^*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

Abstract

Deep DNA or RNA sequencing and posterior mapping to a reference sequence is becoming a standard procedure in molecular biology research. Analyzing millions of mapped reads is a challenging task that doesn't have a unique solution, because experiments using deep sequencing technology vary a great deal among each other. This is why we have developed a flexible tool library called Pyicos, which aims to help biologists in their research when performing their analysis on mapped reads.

Original language	English
Title of host publication	Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers
Pages	83-88
Number of pages	6
DOIs	https://doi.org/10.1007/978-3-642-28062-7_9
Publication status	Published - 2012
Externally published	Yes
Event	10th Spanish Symposium on Bioinformatics for Personalized Medicine, JBI 2010 - Torremolinos, Spain Duration: 27 Oct 2010 → 29 Oct 2010

Publication series

Name	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	6620 LNBI
ISSN (Print)	0302-9743
ISSN (Electronic)	1611-3349

Conference

Conference	10th Spanish Symposium on Bioinformatics for Personalized Medicine, JBI 2010
Country/Territory	Spain
City	Torremolinos
Period	27/10/10 → 29/10/10

Access to Document

10.1007/978-3-642-28062-7_9

Cite this

González-Vallinas, J., Althammer, S., & Eyras, E. (2012). Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing. In Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers (pp. 83-88). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6620 LNBI). https://doi.org/10.1007/978-3-642-28062-7_9

González-Vallinas, Juan ; Althammer, Sonja ; Eyras, Eduardo. / Pyicos : A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing. Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers. 2012. pp. 83-88 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).

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title = "Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing",

abstract = "Deep DNA or RNA sequencing and posterior mapping to a reference sequence is becoming a standard procedure in molecular biology research. Analyzing millions of mapped reads is a challenging task that doesn't have a unique solution, because experiments using deep sequencing technology vary a great deal among each other. This is why we have developed a flexible tool library called Pyicos, which aims to help biologists in their research when performing their analysis on mapped reads.",

keywords = "ChIP-Seq, CLIP-Seq, Deep sequencing, DNA, genomics, High-throughput sequencing, Peak Calling, RNA, software development, transcription factor",

author = "Juan Gonz{\'a}lez-Vallinas and Sonja Althammer and Eduardo Eyras",

year = "2012",

doi = "10.1007/978-3-642-28062-7_9",

language = "English",

isbn = "9783642280610",

series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

pages = "83--88",

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note = "10th Spanish Symposium on Bioinformatics for Personalized Medicine, JBI 2010 ; Conference date: 27-10-2010 Through 29-10-2010",

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González-Vallinas, J, Althammer, S & Eyras, E 2012, Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing. in Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 6620 LNBI, pp. 83-88, 10th Spanish Symposium on Bioinformatics for Personalized Medicine, JBI 2010, Torremolinos, Spain, 27/10/10. https://doi.org/10.1007/978-3-642-28062-7_9

Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing. / González-Vallinas, Juan; Althammer, Sonja; Eyras, Eduardo.
Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers. 2012. p. 83-88 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 6620 LNBI).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

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AU - Althammer, Sonja

AU - Eyras, Eduardo

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AB - Deep DNA or RNA sequencing and posterior mapping to a reference sequence is becoming a standard procedure in molecular biology research. Analyzing millions of mapped reads is a challenging task that doesn't have a unique solution, because experiments using deep sequencing technology vary a great deal among each other. This is why we have developed a flexible tool library called Pyicos, which aims to help biologists in their research when performing their analysis on mapped reads.

KW - ChIP-Seq

KW - CLIP-Seq

KW - Deep sequencing

KW - DNA

KW - genomics

KW - High-throughput sequencing

KW - Peak Calling

KW - RNA

KW - software development

KW - transcription factor

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T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

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González-Vallinas J, Althammer S, Eyras E. Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing. In Bioinformatics for Personalized Medicine - 10th Spanish Symposium, JBI 2010, Revised Selected Papers. 2012. p. 83-88. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). doi: 10.1007/978-3-642-28062-7_9

Pyicos: A flexible tool library for analyzing protein-nucleotide interactions with mapped reads from deep sequencing

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