PMID- 34544141
OWN - NLM
STAT- MEDLINE
DCOM- 20211014
LR  - 20211014
IS  - 2160-1836 (Electronic)
IS  - 2160-1836 (Linking)
VI  - 11
IP  - 9
DP  - 2021 Sep 6
TI  - orthofisher: a broadly applicable tool for automated gene identification and 
      retrieval.
LID - 10.1093/g3journal/jkab250 [doi]
LID - jkab250
AB  - Identification and retrieval of genes of interest from genomic data are an 
      essential step for many bioinformatic applications. We present orthofisher, a 
      command-line tool for automated identification and retrieval of genes with high 
      sequence similarity to a query profile Hidden Markov Model sequence alignment 
      across a set of proteomes. Performance assessment of orthofisher revealed high 
      accuracy and precision during single-copy orthologous gene identification. 
      orthofisher may be useful for assessing gene annotation quality, identifying 
      single-copy orthologous genes for phylogenomic analyses, estimating gene copy 
      number, and other evolutionary analyses that rely on identification and retrieval 
      of homologous genes from genomic data. orthofisher comes complete with 
      comprehensive documentation (https://jlsteenwyk.com/orthofisher/), is freely 
      available under the MIT license, and is available for download from GitHub 
      (https://github.com/JLSteenwyk/orthofisher), PyPi 
      (https://pypi.org/project/orthofisher/), and the Anaconda Cloud 
      (https://anaconda.org/jlsteenwyk/orthofisher).
CI  - © The Author(s) 2021. Published by Oxford University Press on behalf of Genetics 
      Society of America.
FAU - Steenwyk, Jacob L
AU  - Steenwyk JL
AUID- ORCID: 0000-0002-8436-595X
AD  - Department of Biological Sciences, Vanderbilt University , Nashville, TN 37235, 
      USA.
FAU - Rokas, Antonis
AU  - Rokas A
AUID- ORCID: 0000-0002-7248-6551
AD  - Department of Biological Sciences, Vanderbilt University , Nashville, TN 37235, 
      USA.
LA  - eng
SI  - figshare/10.6084/m9.figshare.14399150
GR  - R56 AI146096/AI/NIAID NIH HHS/United States
GR  - HHMI/Howard Hughes Medical Institute/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.
TA  - G3 (Bethesda)
JT  - G3 (Bethesda, Md.)
JID - 101566598
SB  - IM
MH  - Computational Biology
MH  - *Genomics
MH  - Molecular Sequence Annotation
MH  - Sequence Alignment
MH  - *Software
PMC - PMC8496211
OTO - NOTNLM
OT  - *Hidden Markov Model
OT  - *gene family
OT  - *homology
OT  - *orthology
OT  - *phylogenomics
OT  - *sequence similarity search
EDAT- 2021/09/21 06:00
MHDA- 2021/10/15 06:00
CRDT- 2021/09/20 20:32
PHST- 2021/06/07 00:00 [received]
PHST- 2021/07/06 00:00 [accepted]
PHST- 2021/09/20 20:32 [entrez]
PHST- 2021/09/21 06:00 [pubmed]
PHST- 2021/10/15 06:00 [medline]
AID - 6321954 [pii]
AID - jkab250 [pii]
AID - 10.1093/g3journal/jkab250 [doi]
PST - ppublish
SO  - G3 (Bethesda). 2021 Sep 6;11(9):jkab250. doi: 10.1093/g3journal/jkab250.
