Nucleic Acids Research

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Nucleic Acids Research by Mind Map: Nucleic Acids Research

1. 2. RNA sequence databases

1.1. Technology that uses the capabilities of next-generation sequencing to reveal a snapshot of RNA presence and quantity from a genome at a given moment in time.

1.1.1. Rfam

1.1.1.1. The Rfam database provides alignments, consensus secondary structures and covariance models for RNA families.

1.1.1.2. For each ncRNA family, the interface allows users to: view and download multiple sequence alignments; read annotation; and examine species distribution of family members.

1.1.2. Genomic tRNA

1.1.2.1. Contains tRNA gene predictions made by the program tRNAscan-SE on complete or nearly complete genomes.

1.1.3. miRBase

1.1.3.1. Is a database of published miRNA sequences and annotations that provides a centralised system for assigning names to miRNA genes

2. 3. Protein sequence databases

2.1. General sequence databases

2.1.1. UniProt

2.1.1.1. A comprehensive and freely accesible protein sequence database by integrating, interpreting and standardizing data from numerous resources. It consists informations such as gene name, protein sequence/structure/function, expression and cellular location which derived from literature and divide into UniProtKB, UniParc, UnitRef and UniMes.

2.1.1.1.1. Prevent multiple protein data by merging protein sequence based on 100/90/50 identity into a single entry

2.1.1.1.2. Provide blast service to search homology chitinase.

2.1.1.1.3. Manually curated highly-annotated sequences to guide users to choose chitinase.

2.2. Protein properties

2.2.1. SwissSideChain

2.2.1.1. Structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins based on publicly available protein structure in PDB.

2.2.1.1.1. Description on physico-chemical properties (molecular weight, volume, logP, pKa, partial charges, bond/angle/torsion constants) of side chain

2.2.1.1.2. Determination on conformations in crystal structures

3. 4. Structure Databases

3.1. Protein Structure

3.1.1. SWISS-MODEL Repository

3.1.1.1. Database which consist three-dimensional protein models for a set of model organisms from UniProt. SWISS-MODEL workspace allow the template structure searching, model building and models assessment.

3.1.1.1.1. Frequently update on on protein sequence from UniProt cause many new template strucutre and increase quality of modeling of chitinase or other proteins.

3.1.1.1.2. Addition model quality assesment tools enhance the quality in homology modelling for proteins.

3.1.2. RCSB Protein Data Base

3.1.2.1. A curated 3D macromolecular database which can search, visualise and analyze molecule through the web services. The data can be stored by users in a file format(PDB/mmCIF/XML) that consists the details of structure solution, long list of the atoms and their coordinates.

3.1.2.1.1. Functional relationship between chitinase and other proteins can be analysed through sequence and structure alignments.

3.1.2.1.2. Visualisation tool display the strucutre of the protein and atoms, chains and domains.

4. 5. Genomics Databases (non-vertebrate)

4.1. Fungal genome database

4.1.1. Central Aspergillus Data Repository (CADRE)

4.1.1.1. Genomic data for Aspergillus sp. which provides graphical views of assembled sequence and mapped features such as genes and transcripts, allowing comparative analysis of genes

4.1.1.1.1. Provide origins of chitinase, gene sequence encoded for chitinase and the genetic alignments

4.1.1.1.2. Compare chitinase by homologs, paralogs and orthologs in different organisms

5. 6. Metabolic and Signaling Pathways

5.1. Protein-protein interactions

5.1.1. 3D-Interologs

5.1.1.1. The database aims at study orthologous protein-protein interaction with the help of BLAST to scan for proteins with high sequence similarities. It uses the existing information with novel scoring function and structure complexes to generate data of the interested protein based on the protein selected from BLAST.

5.1.1.1.1. from 3D-Inrelogs we can know the evolution and protein- protein interactions of chitinase across multiple species.

5.2. Enzymes and enzyme nomenclature

5.2.1. BRENDA

5.2.1.1. This database provide the information of the enzyme which includes nomenclature, enzyme-ligands interactions, functional parameters, organism related information, enzyme structure, molecular properties, related diseases, references and external link.

5.2.1.1.1. BRENDA show a systematic record and info of various chitinase data from organism to types of reactions it involve

5.3. Signalling pathways

5.3.1. PRRDB

5.3.1.1. The database provides information of pattern recognition receptors and their ligands, where the ligands can be used as adjuvant to improve vaccines function.

5.4. Prokaryotic genome databases

5.5. Metabolic pathways

6. 8. Human Genes and Diseases

6.1. CancerResource

6.1.1. The database provides information of drug and targeted cancer cells. The database retrieve information from PubMed abstract and cancer-related drug-target interactions were from sources such as CTD, PharmGKB, TTD, DrugBank and PDB.

6.2. General human genetics databases

6.2.1. Genetics Home Reference

6.2.1.1. The database provides the information of genetic variation to human health. It includes the gene position on chromosome, product of the gene and other external references.

6.2.1.1.1. can be use to determine chitinase related gene diseases and other related genes.

6.3. General polymorphism databases

6.4. Cancer gene databases

6.5. Gene-, system- or disease-specific databases

7. 9. Microarray Data and other Gene Expression Databases

7.1. GXD-Mouse Gene Expression Database

7.1.1. Community resource for gene expression information from the laboratory mouse.

7.2. Gene Expression Omnibus (GEO)

7.2.1. Public functional genomics data repository that archives and freely distributes microarray, sequencing, and other forms of high-throughput functional genomics data submitted by the research community.

7.2.1.1. GEO DataSets stores original submitter-supplied records (Series, Samples and Platforms)

7.2.1.2. GEO Profile stores gene expression profiles derived from curated GEO DataSets.

8. 10. Proteomics Resources

8.1. BIOZON

8.1.1. Unified biological database that integrates heterogeneous data types such as proteins, structures, domain families, protein–protein interactions and cellular pathways, and establishes the relationships between them.

8.1.1.1. Graphically relate Chitinase to its protein family, nucleic acid sequence and its interaction with other proteins.

9. 11. Other Molecular Biology Databases

9.1. PubMed

9.1.1. A database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals

9.1.1.1. Relationship of AMCase with human disease

10. 12. Organelle databases

10.1. Organelle DB

10.1.1. Compiles protein localization data from organisms spanning the eukaryotic kingdom and presents an organized catalog of the known protein constituents of more than 50 organelles, subcellular structures, and protein complexes.

10.1.2. Organelle View offers a dimensional representation of a yeast cell; users can search Organelle View for proteins of interest, and the organelles housing these proteins will be highlighted in the cell image.

11. 13. Plant databases

11.1. Rice

11.1.1. Oryzabase

11.1.1.1. A database on rice strains of wild type, modified and classical breeding, providing chromosomal maps and gene dictionary for collection of strains and fundamental knowledge on rice science.

11.1.1.1.1. Provide name of gene (CGSNL), origins & trait class of chitinase

11.1.1.1.2. Provide information on gene, trait and plant ontologies of chitinase

11.1.1.1.3. Provide the information on discovery of chitinase (author, journal & reference ID)

11.2. Arabidopsis thaliana

11.2.1. Aramemnon

11.2.1.1. A curated database for Arabidopsis thaliana transmembrane (TM) proteins and transporters with topology and signal sequence predictions and display of results by reliable comparative graphical format.

11.2.1.1.1. Provide information on chitinase sequence, topology and clusters

11.2.1.1.2. Provide gene ontology for chitinase

11.2.1.1.3. Provide data on chitinase expression level on certain plant structures

11.2.1.1.4. View co-expression gene network of chitinase

11.3. General plant database

11.3.1. Phytozome

11.3.1.1. Comparative database for plant genomes by providing evolutionary history of plant gene at the level of sequence, gene structure, gene family and genome organization.

11.3.1.1.1. View information of gene such as locus and transcript name of chitinase

11.3.1.1.2. Able to BLAST & BLAT the selected gene sequence of chitinase

11.3.1.1.3. Compare the homologs of chitinase

11.3.1.1.4. View chitinase as in protein domain and genomic map

11.3.1.1.5. Provide information on gene ancestry of chitinase

12. 14. Immunological databases

12.1. MHCBN

12.1.1. The database provides information about allele specific MHC binding peptides, MHC non-binding, TAP binding, TAP non-binding peptides and T-cell epitopes reported in literature. The newer version is updated with MHC linked autoimmune diseases. It also provides several tools such as Query Searching, TAP Search, Peptide Mapping, Dataset Creation and Similarity Search.

12.1.1.1. helps to identify the chitinase that causes autoimmnue diseases by enzymatic products or environment.

12.2. HaptenDB

12.2.1. The database provides the information of various haptens, which is not immunogenic itself but unless paired with specific antibodies. There are 2021 entries of antibodies and haptens reaction information and 1087 haptens data with 2-D and 3-D structures. Search and analysis tools are also provided.

13. 15. Cell biology

13.1. BARC bd

13.1.1. designed for researchers who require information on how to make best use of valuable biospecimens from biobanks and other sample collections, focusing on the choice of analytical techniques and the demands they make on the type of samples, pre-analytical sample preparation and amounts needed.

13.2. DNAtraffic

13.2.1. Contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling

13.2.2. To create the first platform of the combinatorial complexity of DNA metabolism pathway analysis.

14. 1. Nucleotide sequence database

14.1. International Nucleotide Sequence Database Collaboration

14.1.1. GenBank

14.1.1.1. Publicly available nucleotide sequences generated from sequencing biological molecule in the lab instead of computer-generated string of letters. The availability of sequence is contributed by direct submissions of DNA sequence from original authors. Data of DDBJ and ENA are exchanged daily to ensure the nucleotide sequence are updated.

14.1.1.1.1. -Existence of coding sequence on nucleic acid record ensure the discovery of chitinase or other proteins.

14.1.1.1.2. - Ensure precise information of coding feature on nucleic acid and ensure the data in other database(protein or nucleic acid) can prevent mislead discoveries.

14.2. Coding and non-coding DNA

14.2.1. ACLAME

14.2.1.1. A database which classify and analysis sequence of mobile genetic elements(MGE). Protein families are built from the MGE encoded proteins to provide comprehensive classification of MGE sequence, protein and gene.

14.2.1.1.1. BLAST search interface allow searching sequence

14.2.1.1.2. Provide information of host and its protein families and functions

15. 7. Human and other vertebrate genomes

15.1. Model organisms, comparative genomics

15.1.1. Agbase

15.1.1.1. A database for functional analysis of agricultural plant & animal gene products by developing expressed protein sequence tags (ePSTs) for structural annotation of genomes and Gene Ontology (GO) consortium to describe molecular function, biological process and cellular components for genes and gene products.

15.1.1.1.1. Provide gene ontology annotations in molecular function, biological process and cellular components of plants related to chitinase expression

15.1.1.1.2. Link to various other databases such as EMBL-EBI, UniProt, AmiGO 2 which facilitates during research

15.2. Human genome databases, maps and viewers

15.2.1. UCSC Genome Browser

15.2.1.1. Database of genomic sequence and annotations for organisms such as vertebrates with integrated tools for visualizing, comparing and analyzing genomic data sets. The database offers comparative data such as gene models, regulation, expression and so on

15.2.1.1.1. Show gene sequence, mRNA or genomic alignments and genomic size for chitinase

15.2.1.1.2. Provide information on gene expression and regulation of chitinase

15.2.1.1.3. Able to compare the gene sequence for chitinase among different vertebrates

15.2.1.1.4. Show repeats and variation of the gene sequence for chitinase

15.3. Human ORFs

15.3.1. Mammalian Gene Collection (MGC)

15.3.1.1. Database consisting of cDNA clones containing a full-length open reading frame (FL-ORF) for human, mouse and rat genes. The identified sequence are available in GenBank.

15.3.1.1.1. Provide origins of chitinase and gene sequence

15.3.1.1.2. Able to run BLAST and design primers for cDNA clone for chitinase

15.3.1.1.3. Able to express the chitinase gene in graphical format

16. categories

17. sub category