Gujarat State Leguminosae Family Database (GLDB): Bioinformatics Database of Leguminosae Family present in Gujarat state of INDIA

Sagar S. Patel<sup>1</sup>; Dipti B. Shah<sup>1</sup>; Hetalkumar J. Panchal<sup>2</sup>

Gujarat State Leguminosae Family Database (GLDB): Bioinformatics Database of Leguminosae Family present in Gujarat state of INDIA

Sagar S. Patel¹

, Dipti B. Shah¹

, Hetalkumar J. Panchal²

1. G. H. Patel Post Graduate Department of Computer Science and Technology, Sardar Patel University, Vallabh Vidyanagar, Gujarat-388120, India
2. Gujarat Agricultural Biotechnology Institute, Navsari Agricultural University, Surat, Gujarat- 395007, India

Author

Correspondence author
Computational Molecular Biology, 2014, Vol. 4, No. 11 doi: 10.5376/cmb.2014.04.0011
Received: 10 Dec., 2014 Accepted: 30 Dec., 2014 Published: 07 Jan., 2015

This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Preferred citation for this article:

Patel et al., 2014, Gujarat State Leguminosae Family Database (GLDB): Bioinformatics Database of Leguminosae Family present in Gujarat state of INDIA, Computational Molecular Biology, Vol.4, No.12, 1-13 (doi: 10.5376/cmb.2014.04.0012)

Abstract

Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically data centrally. In present days molecular data are available for many plant species which can be analyzed in relation to taxonomic or evolutionary or affinity context for different plant species. Authors have tried to generate preliminary Bioinformatics data for Leguminosae family species. As much as possible of a particular type of information should be available in one plat form. In short we have made a database which includes all information of Leguminosae family which are found in Gujarat state of India, which contains Botanical information of each species and Bioinformatics information with analysis at one platform. The creation of such kind of database is reflection of interdisciplinary approach for current era where bioinformatics can play major role for botanical database. Which is further extended by developing bioinformatics database and placed all such relevant information on a wide platform for community in general as well as for scientific society in particular.

Keywords

Bioinformatics; Database; Leguminosae family

Bioinformatics has evolved into a full-fledged multidisciplinary subject that integrates developments in information and computer technology as applied to Biotechnology and Biological Sciences. Bioinformatics uses computer software tools for database creation, data management, data warehousing, data mining and global communication networking.

Bioinformatics comprises of annotation, storage, analysis, and searching/retrieval of nucleic acid sequence (genes and RNAs), protein sequence and structural information. This includes databases of the sequences and structural information as well methods to access, search, visualize and retrieve the information.

Bioinformatics concern the creation and maintenance of databases of biological information whereby researchers can both access existing information and submit new entries. Function genomics, biomolecular structure, proteome analysis, cell metabolism, biodiversity, downstream processing in chemical engineering, drug and vaccine design are some of the areas in which Bioinformatics is an integral component.

Leguminosae family is one of the largest family that contains thousands of species of Plants, Herbs, Shrubs, Trees worldwide. This family contains more than 250 species which are found in Gujarat state. There are 3 subfamilies of Leguminosae family which are, Fabaceae (Papilionaceae), Mimosaceae and Caesalpiniaceae.

1 Methods

This database includes Leguminosae family’s each species’ information like its description, taxonomic classification, Locality in Gujarat state, its local name, Pictures, Uses etc. This database also includes Distribution of Leguminosae Family Members in Gujarat state section where different regions of Gujarat state included with Google map followed by list of species which are found in that particular region.

The information contain in this database is from NCBI database and Bioinformatics Analysis of five RNA-Seq Sequences is also done. Data provided in this database is such way that it will be very useful to many people for further study or analysis purpose.

To carry out detailed study of any plant species requires a centrally available data of it. One of the ways to centralize the data is to create a database which could be centrally available and updated regularly according to future requirement.

1.1 Collection of Data

To create any database we need information which is called as Data.Information of all Leguminosae family’s species like it’s description, taxonomic classification, locality, local name, details of fruit and flowers, locality in Gujarat state, uses and pictures were collected from various resources like many Ph.D. thesis, books etc. After compiling and collection of each Leguminosae family’s species we need to create one database for accessing and retrieval of each species data.

Creation of database is necessary while we are dealing with this kind of data. So, we have created database with the help of XAMPP, Dreamweaver and on scripting side PHP language.

2 Results

2.1 Species Information Retrieval Tool

As a part of research, one tool called “Species Information Retrieval Tool” is designed and implemented to get information of species of Leguminosae family which are found in Gujarat state at one click. User has to click on Botanical Information option on left side in GLDB database. Figure 1 is the Home page of GLDB database and Figure 2 is the Home page of Species Information Retrieval Tool, in which species is selected and after click on Submit button it will give full result of that selected particular species (Figure 3).

Figure 1 Home page of GLDB database

Figure 2 Home page of Species Information Retrieval Tool

Figure 3 Result page of Species Information Retrieval Tool

2.2 Distribution of Leguminosae Family Members in Gujarat state

The state is divided into sub zones like Kutch, Saurashtra, North Gujarat, Central Gujarat, South Gujarat and Other region (which includes species found in forests, garden) etc. In addition, Region wise web pages created which gives information of those species which are found in that particular region.

User has to click on Distribution in Gujarat state option on left side in GLDB database. In addition this data are developed by using Bioinformatics approach, so that user will also get location of each region in Google map, as per choice and after click on respective species it will show species’ full description. Figure 4 is Home Page which shows information of Gujarat State and Leguminosae Family with region wise distribution.

Figure 4 Home Page of Gujarat State and Leguminosae Family with region wise distribution

Figure 5 is the information of Kutch region and if user click on any species then it will show result page as shown in Figure 6.

Figure 5 Kutch region Information

Figure 6 Information of species found in Kutch region

2.3 Data and Analysis of Leguminosae Family

This Section introduces Bioinformatics data analysis of Leguminosae family species by tools and data analysis (Figure 7). One tool called “Leguminobase Tool” developed to get information like DNA, PROTEIN, Genome etc of each Leguminosae family species which are found in Gujarat state.

Figure 7 Information of Distribution of Leguminosae family as pie chart

One tool called “ConSeq Tool” also developed to find out any conserved sequence found in submitted sequence.

This chapter also introduces RNA-Seq data analysis of five Leguminosae family species; which is described as “De novo RNA-Seq” data analysis (Table 1 and 2).

Table 1 Information of Distribution of Leguminosae family

Table 2 Information of Leguminobase tool

2.3.1 Leguminobase Tool

There are more than 250 species of this family which are found in Gujarat state of India, out of which information of around 149 Leguminosae family species from NCBI database has been collected and complied. There are three subfamilies of Leguminosae family which are Fabaceae (Papilionaceae), Caesalpiniaceae and Mimosaeae.

In this “Leguminobase Tool” user has to select respective option and after clicking on Submit button it will directly fetch various information from NCBI database like it’s Species Name, PubMed, Pubmed Central, Nucleotide, SRA, PopSet, Genome, BioProject, Protein and Structure information of particular species of Leguminosae family.

Use has to select Bioinformatics Information option on left side in GLDB database and click on Leguminobase Tool. Figure 8 shows the one species which is selected and after click on submit button, it gives various options (Figure 9) and after click on any option, it will fetch data from NCBI database into this GLDB database. Figure 10 shows one of the options which shows the Pubmed option of that particular species.

Figure 8 Leguminobase tool species selection

Figure 9 Result page of Leguminobase tool

Figure 10 Screenshot of Pubmed information from NCBI database in GLDB database

2.3.2 ConSeq Tool

In this ConSeq tool, user has to provide protein sequences of rbcL or matK as input and the tool as a result will provide, user’s sequence followed by its length, Conserved sequence is found in that sequence and based on this conserved sequence the species may be included in one of three subfamilies of Leguminosae family and is it of rbcL or matK protein sequence.

User has to click on Tool option on left side in GLDB database which redirects to home page of ConSeq Tool (Figure 11). If any conserved region found in that sequence then it will show result as shown in Figure 12.

Figure 11 Screen shot of ConSeq Tool

Figure 12 Result page of ConSeq Tool

But if no conserved region found in sequence then ConSeq tool shows output as shown in Figure 13.

Figure 13 Result page of ConSeq Tool when no conserved sequence found

2.3.3 RNA-Seq Data analysis

De novo means assembling short reads to create full-length (sometimes novel) sequences.

De novo sequencing involves sequencing a novel genome for the first time, and requires specialized assembly of sequencing reads. The unique combination of read length, read depth, and flexible paired-end insert sizes makes Illumina sequencers ideal for de novo sequencing. Unparalleled raw read accuracy enables confident and efficient production of high quality, long contig assemblies. Data of both Illumina and Roche 454 are analyzed with five different species.

The detailed analyses of the data set has provided several important features of five species such as GC content, conserved genes across legumes and other plant species, assignment of functional categories by GO terms and identification of SSRs by MISA tool.

It is noted that this study of five different legume species which are Arachis hypogaea L., Cicer arietinum L., Phaseolus vulgaris L., Trigonella foenum-graecum L. and Vicia sativa L. will be useful for further functional genomics studies as it includes useful information of each species with full annotation.

Figure 14 shows the home page of De novo RNA-Seq data page. User has to select first platform either Roche 454 or Illumina then select species in second option and finally select contig. After click on Submit button, it will give full information of that contig as shown in Figure 15. Figure 15 the result of contigs number 10017 of Arachis hypogea L.

Figure 14 Home page for De novo RNA-Seq data retrieval

Figure 15 Result page of de novo RNA-Seq

The result shows various different information of the one contigs from various databases and useful information like, Species Name, Name of contigs, Fasta Sequence, Sequence Length, Blast E-value Min, Blast Similarity Mean, Blast GO number, Top-Hit Species, Blast Hit Description (HSP), Blast Hit Gene Name, Blast Hit Accession, Blast Hit E-value, Blast Hit Length, Blast Hit Align Length, Blast Hit Positives, Blast Hit Similarity, Blast Hsp/Hit, Blast Hsp/Query, Blast Hit Query Frame, Blast Hit Uniprot, Blast Hit Score, Blast Hit GOs, GO Accession, GO Names, Enzyme codes, InterPro Ids, InterPro GO Acession, InterPro GO Names, InterPro Motif Detail, InterPro Motif Matches, Number of Blast Hits, Enzymes, KeggMaps followed by KEGG pathway image if any contigs is involved in any pathway.

There are total 82,505 records of contigs are inserted, which includes 10824 contigs of Arachis hypogaea L., 34678 contigs of Cicer arietinum L., 6999 contigs of Phaseolus vulgaris L., 7256 contigs of Trigonella foenum-graecum L. and 22748 contigs of Vicia sativa L.

3 Glossary

It discusses various botanical terms which are useful to identify any plant species. User has to select Glossary option which is on left side in GLDB database.

4 Publication

This section contains list of Publication which are outcome of this database.

5 References

This section contains list of papers, online site, and books etc which were considered for creating this database.

6 Contact Us

This section contain contact us form in which user can send any questions to us.

7 Conclusion

Database designing of Leguminosae family members in Gujarat state was taken up with following objectives keeping in mind. Like,

ü To bridge the botanical information with the Bioinformatics information and analysis.

ü To utilize various tools of Bioinformatics for analytical purpose for the Leguminosae family species.

ü To generate secondary information from above work with the help of various tools and software available.

ü To provide Bioinformatics information for general public in the form of database.

A comprehensive database for Leguminosae family titled as “Gujarat state Leguminosae family Database (GLDB)” was created with useful information of each species of Leguminosae family.

There are many inbuilt tools developed in this database to get information of particular species like it’s full botanical information along with Distribution of each species of Leguminosae family in Gujarat state with Google map.

While Bioinformatics section comprises of many tools like one tool was designed to get particular species’ DNA, PROTEIN, GENOME etc. information from NCBI database and ConSeq Tool designed to find out any conserved sequences. RNA-Seq data analysis of five Leguminosae family done with de novo sequence assembly & annotation also done.

This particular database of Leguminosae family has served the demands of the present botanical scientific community. So far such information at one platform is not available there by it will serve the purpose of their needs too.

Various scattered data of such Leguminosae family species are placed in such a manner that any person who desire to find information of these particular species will get at one touch or on mouse click.

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