PMID- 26829802
OWN - NLM
STAT- MEDLINE
DCOM- 20180523
LR  - 20240327
IS  - 1557-9964 (Electronic)
IS  - 1545-5963 (Print)
IS  - 1545-5963 (Linking)
VI  - 14
IP  - 5
DP  - 2017 Sep-Oct
TI  - An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in 
      GRO-Seq.
PG  - 1070-1081
LID - 10.1109/TCBB.2016.2520919 [doi]
AB  - We present a fast and simple algorithm to detect nascent RNA transcription in 
      global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol 
      that captures nascent transcripts from actively engaged polymerase, providing a 
      direct read-out on bona fide transcription. Most traditional assays, such as 
      RNA-seq, measure steady state RNA levels which are affected by transcription, 
      post-transcriptional processing, and RNA stability. GRO-seq data, however, 
      presents unique analysis challenges that are only beginning to be addressed. 
      Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes 
      advantage of two popular machine-learning techniques, hidden Markov models and 
      logistic regression, to classify which regions of the genome are transcribed. 
      Given a small user-defined training set, our algorithm is accurate, robust to 
      varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data 
      without a priori need for annotation uncovers surprising new insights into 
      several aspects of the transcription process.
FAU - Azofeifa, Joseph G
AU  - Azofeifa JG
FAU - Allen, Mary A
AU  - Allen MA
FAU - Lladser, Manuel E
AU  - Lladser ME
FAU - Dowell, Robin D
AU  - Dowell RD
LA  - eng
GR  - S10 OD012300/OD/NIH HHS/United States
GR  - T15 LM009451/LM/NLM NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20160126
PL  - United States
TA  - IEEE/ACM Trans Comput Biol Bioinform
JT  - IEEE/ACM transactions on computational biology and bioinformatics
JID - 101196755
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - *Algorithms
MH  - Computational Biology/*methods
MH  - Databases, Genetic
MH  - Humans
MH  - Markov Chains
MH  - Molecular Sequence Annotation/*methods
MH  - RNA/analysis/*genetics
MH  - Sequence Analysis, RNA/*methods
PMC - PMC5667649
MID - NIHMS912031
EDAT- 2016/02/02 06:00
MHDA- 2018/05/24 06:00
PMCR- 2018/09/01
CRDT- 2016/02/02 06:00
PHST- 2016/02/02 06:00 [pubmed]
PHST- 2018/05/24 06:00 [medline]
PHST- 2016/02/02 06:00 [entrez]
PHST- 2018/09/01 00:00 [pmc-release]
AID - 10.1109/TCBB.2016.2520919 [doi]
PST - ppublish
SO  - IEEE/ACM Trans Comput Biol Bioinform. 2017 Sep-Oct;14(5):1070-1081. doi: 
      10.1109/TCBB.2016.2520919. Epub 2016 Jan 26.