**Main Bioinformatics Databases**
1. GenBank: A comprehensive public database of nucleotide sequences and supporting bibliographic and biological annotation.
2. EMBL: European Molecular Biology Laboratory's Nucleotide Sequence Database, similar to GenBank.
3. DDBJ: DNA Data Bank of Japan, part of the International Nucleotide Sequence Database Collaboration.
4. UniProt: A central repository for protein sequence and function.
5. PDB: Protein Data Bank, a repository for the 3D structural data of large biological molecules.
6. KEGG: Kyoto Encyclopedia of Genes and Genomes, a database for understanding high-level functions and utilities of the biological system.
7. NCBI PubMed: A database for biomedical literature, including research papers.
8. BLAST: Basic Local Alignment Search Tool, for comparing primary biological sequence information.
9. Ensembl: A genome browser for vertebrate genomes.
10. Swiss-Prot: A manually annotated and reviewed protein sequence database.
**Additional Bioinformatics Databases**
11. STRING: A database of known and predicted protein-protein interactions.
12. Reactome: A database of biological pathways.
13. GEO (Gene Expression Omnibus): A public repository for gene expression datasets.
14. TCGA (The Cancer Genome Atlas): A project to catalogue genetic mutations responsible for cancer.
15. Pfam: A database of protein families and domains.
16. RCSB PDB (Research Collaboratory for Structural Bioinformatics Protein Data Bank): An expanded resource for the exploration of biological macromolecule structures.
17. InterPro: Provides functional analysis of proteins by classifying them into families and predicting domains and important sites.
18. OMIM (Online Mendelian Inheritance in Man): A comprehensive database of human genes and genetic phenotypes.
19. ArrayExpress: A database of functional genomics experiments.
20. ChEMBL: A manually curated database of bioactive molecules with drug-like properties.
**Main Bioinformatics Software and Tools**
21. BLAST (Basic Local Alignment Search Tool): Used for comparing nucleotide or protein sequences to sequence databases.
22. Clustal: A widely used tool for multiple sequence alignment.
23. Bioconductor: An open-source software project for the analysis and comprehension of genomic data, primarily based on R programming language.
24. BioPerl, BioPython, BioJava: Libraries for bioinformatics, available in Perl, Python, and Java languages respectively.
25. Cytoscape: A software platform for visualizing molecular interaction networks and biological pathways.
26. GATK (Genome Analysis Toolkit): A software package for analyzing next-generation sequencing data.
27. MEGA (Molecular Evolutionary Genetics Analysis): Software for conducting statistical analysis of molecular evolution.
28. HMMER: Used for searching sequence databases for sequence homologs, and for making sequence alignments.
29. R (and RStudio): Popular for statistical computing and graphics, widely used in bioinformatics for data analysis.
30. Galaxy: An open-source, web-based platform for data-intensive biomedical research.
**Additional Bioinformatics Software and Tools**
31. SAMtools: Tools for manipulating alignments in the SAM format.
32. Bowtie/Bowtie2: Ultrafast, memory-efficient tools for aligning sequencing reads to long reference sequences.
33. BWA (Burrows-Wheeler Aligner): Software package for mapping low-divergent sequences against a large reference genome.
34. TopHat: A fast splice junction mapper for RNA-Seq reads.
35. Cufflinks: Software for analyzing RNA-Seq data to assemble transcripts, estimate their abundances, and detect differential expression.
36. UCSC Genome Browser: An interactive web-based tool used for the visualization and analysis of genomic data.
37. MUMmer: A system for rapidly aligning entire genomes.
38. BEDTools: A powerful toolset for genome arithmetic.
39. IGV (Integrative Genomics Viewer): A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
40. Qiime: A pipeline for performing microbiome analysis from raw DNA sequencing data.
