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ISSN: 2682-4043
DOI:10.36462/H.BioSci.20195

Highlights in BioScience October 2019| Volume 2
http://bioscience.highlightsin.org/

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Research Article

Open Access

1 Department of Genome Mapping, Molecular
Genetics and Genome Mapping Laboratory,
Agricultural Genetic Engineering Research
Institute, Giza, Egypt.
2 International Center for Agricultural Research in
the Dry Areas (ICARDA), Cairo, Egypt.

Contacts of Authors

* To whom correspondence should be
addressed: Alsamman M. Alsamman.

Citation: Alsamman M.A. , Habib P.T. (2019).
GeneSyno : Simple tool to extract gene sequence
from the human genome despite synonymous
gene terms. Highlights in BioScience, Volume 2 .
Article ID 20195, dio:10.36462/ H.BioSci.20195

Received: August 25, 2019

Accepted: September 20, 2019

Published: October 25, 2019

Copyright: © 2019 Alsamman and Habib. This
is an open access article distributed under the
terms of the Creative Commons Attribution
License, which permits unrestricted use,
distribution, and reproduction in any medium,
provided the original author and source are
credited.

Data Availability Statement: All relevant data
are within the paper and supplementary materials

Funding: The authors have no support or
funding to report.

Competing interests: The authors declare that
they have no competing interests.

GeneSyno : Simple tool to extract gene sequence from the
human genome despite synonymous gene terms

Alsamman M. Alsamman1* , Peter T. Habib2

Abstract
Extracting gene data from the human genome is a tricky task. Gene

name is the key information for harvesting its sequence, annotation, and
other related data.Unfortunately, most human genes have different and
multiple names, depending on the database and the resource in which they
have been published. Such an issue is delaying the ability of researchers to
gather the necessary knowledge and to build their opinion on the function
of genes. Here we introduce GeneSyno, a simple, versatile and reliable tool
that can be used to extract gene information from human genome data even
though it is synonymous gene names. GeneSyno was written using C and
Python programming languages and could easily be integrated into another
pipeline.

Keywords: gene information, human genome, gene name , gene annotation, gene,
synonymous gene name.

Background

Human Genome Research is one of the most intensive research fields.
Synonymous terms of the name of the gene remain a major issue in human
genomics (1). Several human genes have different names, depending on the
databases, the articles or the newly discovered function. With even more research
articles published online, this information has become challenging for efficient
implementation and reuse (2). Such a case has been a complicated issue where
genomic scientists can not form a collective and prospective conclusion by using
published information on most human genes.

Several tools have been published to solve this problem, where text
mining, and searching for databases could be used to generate symbol
co-occurrences to extend information extraction capabilities (3-6).The main
problem that, most of these tools require high computational skills, or are
available only in online versions. Most of these tools require high computational
skills, or are only available in online versions. This may constrain the ability of
researchers to access all available information for massive lists of genes at any
time.

Here we introduce GeneSyno, a simple, versatile and reliable tool that can
be used to extract gene information from human genome data even though it is
synonymous gene names. GeneSyno was written using C and Python
programming languages and could easily be integrated into another pipeline.

Material and methods
GeneSyno was built using C and Python3 programming languages. The

user’s input will be a list of human gene names. The input from the user will be a
list of names for human genes. GeneSyno collects all available information about
these genes from the GRCh38 database (which users could change for newer
versions) and reports a tab-limited file containing gene information such as gene
name, official gene name, chromosome , description, gene start, gene end, and a
list of gene synonym names. Furthermore, it produced a FASTA file that contains
sequences of all genes' proteins . If gene have more than one protein (isoforms) it
will reported (Figure 1).

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Alsamman et al., 2019 GeneSyno : Simple tool to extract gene information despite synonymous gene terms

Highlights in BioScience October 2019| Volume 2
http://bioscience.highlightsin.org/

GeneSyno core was written using C programming
language to extract massive lists of information about genes
in less processing time. GeneSyno can be installed and used
on various operating systems, and has a simple GUI for
users.

Figure 1 : Example of GeneSyn input and outputs. If a list of names of human genes is given in text format (A), GeneSyno can
produce a table containing all gene information in tab delimited format (B) and protein sequences in FASTA formats (C) .

Availability
GeneSyno is available as a standalone tool at :

https://github.com/AlsammanAlsamman/GeneSyno

References
1. Cohen KB, Acquaah-Mensah GK, Dolbey AE, Hunter L.
Contrast and variability in gene names. In: Proceedings of
the ACL-02 workshop on Natural language processing in
the biomedical domain-Volume 3. 2002. p. 14–20.

2. Chen L, Liu H, Friedman C. Gene name ambiguity of
eukaryotic nomenclatures. Bioinformatics.
2005;21(2):248–56.

3. Cohen AM, Hersh WR, Dubay C, Spackman K. Using
co-occurrence network structure to extract synonymous
gene and protein names from MEDLINE abstracts. BMC
Bioinformatics. 2005;6(1):103.

4. Plotkin JB, Kudla G. Synonymous but not the same: the
causes and consequences of codon bias. Nat Rev Genet.
2011;12(1):32–42.

5. Girish K, Dubey S. Eukaryotic Molecular Biology
Databases: An Overview. Highlights Biosci. 2018;1:1–7.

6. Alsamman AM. The Art of Bioinformatics Learning in
Our Arabic World. Highlights Biosci. 2019;2.

https://github.com/AlsammanAlsamman/GeneSyno
http://bioscience.highlightsin.org/

