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10 Favorite Online Tools for Molecular Biology

What did we do before the internet? And where would we be without handy online molecular biology tools?

Apparently in the ‘olden days’ doing a simple gene or protein alignment required programs that used dynamic programming algorithms such as the Needleman-Wunsch and Smith-Waterman algorithms. These required long processing times and the use of supercomputers or parallel computer processors. Sound complicated?

Nowadays, molecular biology tools are much more accessible – thank goodness!

Here are some of my favorite online sites for molecular biology:

1.  BLAST (NCBI): The Basic Local Alignment Search Tool (BLAST) is an algorithm for comparing primary sequence information. A BLAST search allows you to compare a sequence of interest with a database of sequences for homology.  It can be used to align different types of sequences such as amino acids or nucleotides.

2.  Ensembl: The Ensembl concept lies in the ability to automatically generate graphical views of gene alignment (and other data) against a reference genome. The nice thing about Ensembl is that you can turn on and off certain features or ‘tracks’ depending on what you want to see. It is also really useful in obtaining some basic information, like transcript length, coding exon number and even GO details.

3.  Primer 3: This is a great online tool to help you pick primers. It takes in to account your desired Tm, product size and many more variables.  Find it here: http://biotools.umassmed.edu/bioapps/primer3_www.cgi.

4.  GEO (NCBI): The Gene Expression Omnibus (GEO) is yet another of the array of tools that NCBI offers. It is basically a public functional genomics repository that archives and freely distributes microarray, next-generation sequencing, and other forms of high-throughput functional genomics data submitted by the research community. Some journals are now beginning to request that your microarray data be available on this site before publication. This is a really great tool to see how gene expression changes under many different conditions and in many different species.

5.  UniProt: This is a high quality and freely accessible database of protein sequence and functional information. Many of the entries are derived from genome sequencing projects and it contains a large amount of information about the biological function of proteins derived from research literature. See: http://www.uniprot.org/.

6.  Ingenuity Pathway Analysis (IPA): One of the great things about IPA is that it can be used with or without data. It can help in the analysis of data from expression and SNP microarrays, proteomics and any experiment that generates a gene list, in order to get an insight into molecular interactions, phenotypes and disease processes. IPA also allows you to search for specific information on genes, proteins drugs etc. that can be used to build models or design experiments. Although it is not free, it can be used for a free trial period. Find it here: http://www.ingenuity.com/products/ipa.

7.  Reactome: This is a manually curated, peer-reviewed database of biomolecular pathways. It can be used for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis and systems biology.

8.  GeneMANIA: Apart from the fun name, this site is quite useful. It finds genes that are related to a single or group of input genes using a large set of functional association data.  This includes protein/gene interactions, co-expression and co-localization data. Find it here: http://www.genemania.org.

9.  Restriction Mapper: This tool maps sites for restriction enzymes, like endonucleases, in DNA sequences. It even does a ‘virtual digestion’.

10. Molecular Biology Protocols Online: Although this is not really a program or tool, it can be really useful if you need some protocol hints. It has everything from RNA extraction to transfection to cloning. Find it here: http://www.protocol-online.org/prot/Molecular_Biology/.

This is only just a small percentage of the tools out there. We’d love to hear about some of the great online tools you have found!

8 Comments

  1. merve on January 29, 2019 at 1:14 am

    I love your website! Thank you so much for the content!

  2. Tim Hulsen on January 10, 2019 at 7:33 pm

    Don’t forget http://www.biovenn.nl, for creating area-proportional Venn diagrams using gene lists.

  3. Smockus on July 14, 2016 at 11:01 am

    JAX-CKB (ckb.jax.org) is a great resource for variant interpretation of cancer related next-generation sequencing data.

  4. EMIL on April 7, 2016 at 3:57 pm

    Some other very useful free online tools can be found at http://www.molbiotools.com.

  5. nurul on December 16, 2015 at 12:58 am

    Great article. I used to use some of these software (Blast n primer3) with good results. Some software like GEO, genemania and reactome make me more confuse than before.

  6. Kerstin Bern on May 8, 2014 at 5:06 am

    Many of these tools listed here are limited to VERY few or a single organism! So is also genecards, mentioned above.

    • Rebecca Tirabassi on May 13, 2014 at 11:56 am

      Do you have some suggestions for ones that are more general?

  7. es7674 on May 6, 2014 at 3:33 am

    Great article! I also highly recommend http://www.genecards.org/ . I almost always have it open when reading the literature, as it allows you to instantly get an outline of the known functions, features, domains, expression patterns, splice variants, etc., of any gene I encounter. Search the name or acronym of any gene/protein and it will bring up a page including information compiled from many sources. One of my favorite features (and one of the simplest) is the list of gene/protein aliases for each entry, which has saved me hours of searching the literature for information about genes using obscure acronym.

    Another must is the UCSC Genome Browser. Use this intuitive interface to surf the genome looking at graphically displayed data from many sources, including most of the data from ENCODE. Exploring regulation of a new gene? A quick search for the gene, turn on a few fields, and you can see, all at once, which tissues it is expressed in, the chromatin state(marks) at the locus, the transcription factors/enhancers that bind its promoter, and countless other valuable data.

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