Dataset Information

Peptide Combination Generator: a Tool for Generating Peptide Combinations.

ABSTRACT: Peptides are used as reagents both for basic research and diagnostic purposes. Therefore, there is a need for novel methods for the design of peptide molecules with a particular specific physiochemical profile. The properties of the peptides are governed by the nature of amino acids constituting the peptide. There is a lack of a web server or tools which could predict all the possible combinations of the peptides generated because of the combinations of amino acids based on the physiochemical properties. We have developed a peptide combination generator (PepCoGen), a web server for generating all the possible combinations of peptides by varying the amino acids having similar physiochemical properties at a particular position. It also predicts other properties of the peptides including molecular weight, charge, solubility, hydrophobic plot, and isoelectric point, and random three-dimensional models for each generated combination.

SUBMITTER: Ali N

PROVIDER: S-EPMC7097909 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature

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Peptide Combination Generator: a Tool for Generating Peptide Combinations.

Ali Naseem N Shamoon Arzoo A Yadav Neelesh N Sharma Tanuj T

ACS omega 20200316 11

Peptides are used as reagents both for basic research and diagnostic purposes. Therefore, there is a need for novel methods for the design of peptide molecules with a particular specific physiochemical profile. The properties of the peptides are governed by the nature of amino acids constituting the peptide. There is a lack of a web server or tools which could predict all the possible combinations of the peptides generated because of the combinations of amino acids based on the physiochemical pr ...[more]

PMID: 32226857

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Project description:BackgroundRapid generation of omics data in recent years have resulted in vast amounts of disconnected datasets without systemic integration and knowledge building, while individual groups have made customized, annotated datasets available on the web with few ways to link them to in-lab datasets. With so many research groups generating their own data, the ability to relate it to the larger genomic and comparative genomic context is becoming increasingly crucial to make full use of the data.ResultsThe Omics Database Generator (ODG) allows users to create customized databases that utilize published genomics data integrated with experimental data which can be queried using a flexible graph database. When provided with omics and experimental data, ODG will create a comparative, multi-dimensional graph database. ODG can import definitions and annotations from other sources such as InterProScan, the Gene Ontology, ENZYME, UniPathway, and others. This annotation data can be especially useful for studying new or understudied species for which transcripts have only been predicted, and rapidly give additional layers of annotation to predicted genes. In better studied species, ODG can perform syntenic annotation translations or rapidly identify characteristics of a set of genes or nucleotide locations, such as hits from an association study. ODG provides a web-based user-interface for configuring the data import and for querying the database. Queries can also be run from the command-line and the database can be queried directly through programming language hooks available for most languages. ODG supports most common genomic formats as well as generic, easy to use tab-separated value format for user-provided annotations.ConclusionsODG is a user-friendly database generation and query tool that adapts to the supplied data to produce a comparative genomic database or multi-layered annotation database. ODG provides rapid comparative genomic annotation and is therefore particularly useful for non-model or understudied species. For species for which more data are available, ODG can be used to conduct complex multi-omics, pattern-matching queries.

Dataset Information

Peptide Combination Generator: a Tool for Generating Peptide Combinations.

Publications

Peptide Combination Generator: a Tool for Generating Peptide Combinations.

Similar Datasets

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