Cunningham Memorial Library: BIO 609: Finding Datasets

Phylogenetic Data

MEGA
MEGA: Molecular Evolutionary Genetics Analysis Software
FREE for use in research and education
"an integrated tool for conducting sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses"
Clustal Omega
"Clustal Omega is a general purpose multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments for proteins and DNA."
M-Coffee
"Rather than computing a multiple sequence alignment on its own, it uses other packages to compute the alignments. It then uses T-Coffee to combine all these alignments into one unique final alignment"
PhyML
Phylogeny software that analyzes large collections of real nucleotide and amino-acid data sets of various sizes.

miRNA

miRNA
Online database for miRNA target prediction and functional annotations for five species: human, mouse, rat, dog and chicken.
miRBase
Database of published miRNA sequences and annotation

NCBI Databases

The National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources that include the GeneBank, Entrez, MyNCBI, PubMed, Entrez Gene, BLAST, BLAST Link (BLink), Electronic PCR, UniGene, HomoloGene, ProtEST, Cancer Chromosomes, Entrez Genomes, among many others.

National Center for Biotechnology Information - NCBI
DNA & RNA - Site Guide - NCBI
The NCBI Handbook. 2nd edition.
NCBI Help
GenBank Sample Record
Includes description of each data element or field
About RefSeq
Querying GEO DataSets and GEO Profiles
GEO stand for "Gene Expression Omnibus."
OMIM Search Help
NCBI Genome Browsers YouTube Playlist
National Libraries of Medicine
NCBI Workshops, Webinars, Codeathons & Conferences
NCBI, National Library of Medicine
NCBI Documentation
Help, FAQ, and factsheets for specific NCBI databases

PubMed includes over 26 million citations for biomedical literature from MEDLINE, life science journals, and online books. PubMed citations and abstracts include the fields of biomedicine and health, covering portions of the life sciences, behavioral sciences, chemical sciences, and bioengineering. Select full-text is available via PubMed Central.

PubMed Online Training
Tutorials from the National Libraries of Medicine. Brief or long. Novice or advanced.
How PubMed® Works
Recordings and PowerPoints of a series of four in depth National Library of Medicine training workshops of 2023.
Using PubMed in Evidence-Based Practice
Learn to develop a clinical question using PICO & efficiently find relevant biomedical literature using PubMed. About 30 minutes to complete.
PubMed Help
Very thorough e-book. National Center for Biotechnology Information (US). Updated to the present.
The New PubMed is Here
Collins M. The New PubMed is Here. NLM Tech Bull. 2019 Nov-Dec;(431):e3. Tells what changed.
Medical Genetics Search Filters in PubMed
Search queries for medical genetics topics programmed into PubMed.
PubMed Search Algorithm
The algorithm is the set of rules a search engine uses to retrieve and rank results.
Exporting References from PubMed into EndNote
How to export records from PubMed into EndNote, the bibliographic management database that helps you format citations
Medical Subject Headings 2020 - MeSH Browser
Look up Medical Subject Headings in the MeSH database to choose them for your search in MEDLINE

Miscellaneous Bioinformatics Tools

BioNumbers
Database of numbers in molecular and cell biology. Whenever you need the size of a cell, metabolite concentrations, reaction rates and times, number of mitocondria in a cell, etc, check this database.
BRENDA
BRENDA is FREE collection of enzyme functional data.
Cancer Genome Atlas Data Portal - TCGA
The Cancer Genome Atlas Data Portal (TCGA) allows you search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes
GeneMark
GenMAPP
Gene Map Annotator and Pathway Finder visualizes gene expression and genomic data on maps of biological pathways and groupings of genes.
LigerCat
Searches PubMed, builds a Tag Cloud, and calculates frequency of MeSH terms.
PATRIC
Pathosystems Resource Integration Center is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division. bacterial infectious diseases via integration of vital pathogen information with data and analysis tools

Plant Bioinformatics Databases

SoyBase
SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean.
SALAD
SALAD is a motif-based database of protein annotations for plant comparative genomics. Contains information on proteome data sets of rice, sorghum, Arabidopsis thaliana, grape, a lycophyte, a moss, algae, and yeast.
Plant Transcription Factor Database - PlnTFDB
The Plant Transcription Factor Database (PlnTFDB) provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators in plant species whose genomes have been completely sequenced and annotated.
Plant microRNA Database - PMRD
The Plant microRNA Database (PMRD) integrates available plant miRNA data deposited in public databases, collected from the literature, and data generated in-house.

Data Sources

DNA & RNA - Site Guide - NCBI

There are many free bioinformatics data sources on the Internet. Many of them are "mirror sites," which are duplicated sites. Mirror sites help direct traffic from overloading one site and help preserve the data by making multiple copies of it.

UCSC Genome Bioinformatics
U.S. Government Collected Data Sets
equinegenome.org
Horse genome database
BLAST
- This link opens in a new window
"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families."
The International Nucleotide Sequence Database Collaboration
Instructions for individuals to submit data to the international sequence databases of DNA Databank of Japan (DDOJ), European Nucleotide Archive (EMBL-EBI), and the National Center for Biotechnology Information (NCBI) of the United States.

International Data Sources

The European Bioinformatics Institute
This European bioinformatics system utilizes BLAST or FASTA programs for sequence similarity- homology analysis; InterProScan for motifs analysis; ClustalW2 for sequence alignment; MSDfold for protein structure query and comparison.
DNA Data Bank of Japan (DDBJ)
Stores sequence data mainly from Japanese researchers.
National BioResource Project (NBRP)
The Japanese National BioResource Project (NBRP) is a group of 30 databases under an integrated database-retrieval system (BioResource World: BRW) . It provides access to bioresources for use as experimental materials for life science research.

Subject Guide

Shelley Arvin

Email Me

Contact:

Cunningham Memorial Library, rm 113

1-812-237-2605

Netherlands Bioinformatics Centre

PATRIC

PATRIC
Pathosystems Resource Integration Center is a NIH-NIAID -funded project of Virginia Tech’s Cyberinfrastructure Division. bacterial infectious diseases via integration of vital pathogen information with data and analysis tools

GenMAPP

GenMAPP
Gene Map Annotator and Pathway Finder visualizes gene expression and genomic data on maps of biological pathways and groupings of genes.

Bionumbers

BioNumbers
Database of numbers in molecular and cell biology. Whenever you need the size of a cell, metabolite concentrations, reaction rates and times, number of mitocondria in a cell, etc, check this database.

Brenda

BRENDA
BRENDA is FREE collection of enzyme functional data.

Dataset Databases and Websites

Explore the British Library

Finding sequences of DNA, RNA, or proteins.

Data Annotation

GeneMark

Cancer Genome Atlas Data Portal

Cancer Genome Atlas Data Portal - TCGA
The Cancer Genome Atlas Data Portal (TCGA) allows you search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high-throughput sequencing analysis of the tumor genomes