PMID- 30014738
OWN - NLM
STAT- MEDLINE
DCOM- 20190808
LR  - 20190808
IS  - 1940-9818 (Electronic)
IS  - 0736-6205 (Linking)
VI  - 65
IP  - 1
DP  - 2018 Jul
TI  - A bioinformatics approach to identify telomere sequences.
PG  - 20-25
LID - 10.2144/btn-2018-0057 [doi]
AB  - Conventional approaches to identify a telomere motif in a new genome are 
      laborious and time-intensive. An efficient new methodology based on 
      next-generation sequencing (NGS), de novo sequence repeat finder (SERF) and 
      fluorescence in situ hybridization (FISH) is presented. Unlike existing heuristic 
      approaches, SERF utilizes an exhaustive analysis of raw NGS reads or assembled 
      contigs for rapid de novo detection of conserved tandem repeats representing 
      telomere motifs. SERF was validated using the NGS data from Ipheion uniflorum and 
      Allium cepa with known telomere motifs. The analysis program was then used on NGS 
      data to investigate the telomere motifs in several additional plant species and 
      together with FISH proved to be an efficient approach to identify as yet unknown 
      telomere motifs.
FAU - Somanathan, Indira
AU  - Somanathan I
AD  - Department of Biological Sciences, California State University East Bay, Hayward, 
      CA, USA.
FAU - Baysdorfer, Chris
AU  - Baysdorfer C
AD  - Department of Biological Sciences, California State University East Bay, Hayward, 
      CA, USA.
LA  - eng
PT  - Journal Article
PL  - England
TA  - Biotechniques
JT  - BioTechniques
JID - 8306785
MH  - Allium/*genetics
MH  - Amaryllidaceae/*genetics
MH  - *Computational Biology
MH  - Conserved Sequence/genetics
MH  - High-Throughput Nucleotide Sequencing
MH  - In Situ Hybridization, Fluorescence
MH  - Nucleotide Motifs/genetics
MH  - Sequence Analysis, DNA
MH  - Tandem Repeat Sequences/genetics
MH  - Telomere/*genetics
OTO - NOTNLM
OT  - NGS
OT  - SERF
OT  - bioinformatics
OT  - next-generation sequencing
OT  - sequence repeat finder
OT  - tandem repeats
OT  - telomere
EDAT- 2018/07/18 06:00
MHDA- 2019/08/09 06:00
CRDT- 2018/07/18 06:00
PHST- 2018/07/18 06:00 [entrez]
PHST- 2018/07/18 06:00 [pubmed]
PHST- 2019/08/09 06:00 [medline]
AID - 10.2144/btn-2018-0057 [doi]
PST - ppublish
SO  - Biotechniques. 2018 Jul;65(1):20-25. doi: 10.2144/btn-2018-0057.