BESTORF specifications

Information


Unique identifier OMICS_17958
Name BESTORF
Interface Web user interface
Restrictions to use None
Input format FASTA
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Victor Solovyev <>

BESTORF in publications

 (10)
PMCID: 4298115
PMID: 25597920
DOI: 10.1186/s12870-014-0369-1

[…] by clustalw (http://www.ebi.ac.uk) and blast (http://blast.ncbi.nlm.nih.gov). gene structure prediction was performed by the fgenesh on-line tool (http://linux1.softberry.com/cgi-bin/programs/gfind/bestorf.pl)., total rna was isolated from spikes of infected and mock-inoculated (control) plants of both resistant 02-5b-318 and susceptible saragolla at 24, 48 and 72 hours post inoculation. […]

PMCID: 4100101
PMID: 24871367
DOI: 10.3390/ijms15069386

[…] the noncode database [] and the ncbi “nt” nucleotide database. second, for the transcripts without homology to the above databases, we predicted their putative open reading frames (orfs) using bestorf (http://linux1.softberry.com/berry.phtml?topic=bestorf&group=programs&subgroup=gfind). because species-specific protein-coding genes exist, these genes could not be identified using […]

PMCID: 3852720
PMID: 24112604
DOI: 10.1186/1471-2164-14-695

[…] rna-seq short reads were assembled into transcript contigs de novo (i.e., independent of the reference genome sequence) using inchworm [] and open reading frames extracted from the transcripts with bestorf (molquest package, softberry). the de novo transcript assembly was input into pasa [] to refine the alignment-based gene models with mrna evidence (figure ). the three data sets […]

PMCID: 3701547
PMID: 23799877
DOI: 10.1186/1471-2164-14-415

[…] with the standard codon table using custom perl scripts. for those transcripts without any blastx hit against known databases, the best potential coding region was predicted using the software bestorf with parameters trained on arabidopsis ests. the predicted amino sequences were submitted to search against the pfam database (version 25.0) [] for domain/family annotation using hmmer 3.0, […]

PMCID: 3320591
PMID: 22496661
DOI: 10.1371/journal.ppat.1002643

[…] preparation, sequencing techniques, strategies to maximize gene discovery as well as est assembly statistics can be found in . orfs were predicted from est contigs with the fusarium matrix of bestorf (molquest package, softberry). solubly secreted proteins were identified following published guidelines . secreted proteins (and their corresponding contigs) for which no significant […]


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