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chevron_left Variant effect prediction Gene prediction Multiple nucleotide sequence alignment Secondary structure prediction Protein-coding gene prediction Structural motif detection Protein-DNA interaction prediction Subcellular localization prediction Pairwise nucleotide sequence alignment Bioinformatics workflows chevron_right
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MolQuest specifications


Unique identifier OMICS_26975
Name MolQuest
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Medium
Version 2.4.5
Stability Stable
Maintained Yes




No version available



  • person_outline MolQuest Team

MolQuest citations


An improved draft of the pigeonpea (Cajanus cajan (L.) Millsp.) genome

PMCID: 5723258
PMID: 29234695
DOI: 10.1016/j.dib.2017.11.066

[…] edict the protein coding genes the improved draft assembly was first repeat-masked using RepeatModler and RepeatMasker software , followed by ab-initio gene prediction using the FGENESH module of the Molquest v. 4.5 software package ( The predicted genes were annotated using BLASTX (E<10-6) search against the NCBI non-redundant (nr) protein database using Blast2GO softwa […]


Computational deciphering of biotic stress associated genes in tomato (Solanum lycopersicum)

Genom Data
PMCID: 5643083
PMID: 29062693
DOI: 10.1016/j.gdata.2017.09.003

[…] The unannotated Contigs were used as input in FGENESH program of Molquest. It was observed that when Solanum lycopersicum was used as reference genome total 58 genes were predicted for Velvet Contigs and 38 genes for Contigs of EGassembler. But when Nicotiana tabac […]


A Genome Wide Prediction and Identification of Intergenic Small RNAs by Comparative Analysis in Mesorhizobium huakuii 7653R

Front Microbiol
PMCID: 5596092
PMID: 28943874
DOI: 10.3389/fmicb.2017.01730

[…] Searches for promoters in the M. huakuii 7653R genome were performed using Promoter 2.0 ( and BPROM ( Predictions of Rho-independent terminators were implemented with RNAMotif 3.0.7 (, TransTermHP 2.09 (, FindTerm […]


The draft genome of Corchorus olitorius cv. JRO 524 (Navin)

Genom Data
PMCID: 5432662
PMID: 28540183
DOI: 10.1016/j.gdata.2017.05.007

[…] were merged using PANDASeq v2.7 , and then assembled de novo using Newbler v. 2.6 with default parameters (Roeche Inc. Germany). We used the FGENESH gene prediction pipeline from the software package Molquest v4.5 ( for the in silico prediction of genes. The predicted genes were annotated using BLASTX (E < 10− 6) search against the NCBI non-redundant (nr) protein database. […]


Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing

Sci Rep
PMCID: 5314344
PMID: 28211474
DOI: 10.1038/srep42419

[…] The repeat elements belonging to various classes including long terminal repeats (LTRs), non-LTRs, and DNA transposon elements were identified using MapRep (MolQuest2). Out of the total transposable elements (TEs) identified nucleotide sequences greater than 200 bp for two major groups (i.e. Gypsy and Copia) were extracted from their respective contigs. T […]


Transcriptome analysis of smooth cordgrass (Spartina alterniflora Loisel), a monocot halophyte, reveals candidate genes involved in its adaptation to salinity

BMC Genomics
PMCID: 4992267
PMID: 27542721
DOI: 10.1186/s12864-016-3017-3

[…] etra, penta and hexa-nucleotides were used to design ESSR primers as described earlier []. The positions of the SSRs on open reading frames of the genes were determined by using gene finding software MolQuest (FGENESH+; Predictive function of the sequences containing SSR motifs were retrieved from the MySQL database containing information on functional ann […]

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