How to use the web for bioinformatics
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How to use the web for bioinformatics. Ethan Strauss [email protected] 274-4330 X 1171 Objectives. At the end of this session you should be able to do all of the following freely available tools on the world wide web:

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How to use the web for bioinformatics

How to use the web for bioinformatics

Ethan Strauss

[email protected]

274-4330 X 1171



At the end of this session you should be able to do all of the following freely available tools on the world wide web:

Use Genbank or a similar database to find nucleic acid sequences of interest

Understand the parts of a Genbank entry

Use a BLAST server (e.g. ) to find related sequences.

Perform an alignment of several nucleic acid sequences

Obtain the protein sequence which corresponds to a specific Nucleic acid sequence

How to find all those dang urls

How to find all those dang URLs!




  • Sequence Databases

    • What does a Genbank Entry look like?

  • Translation and other Utilities


  • Multiple Sequence Alignment

  • PCR Primer Design

Sequences databases

Sequences Databases

  • NCBI databases – Nucleic acids, proteins, Literature, genomes, taxonomy, SNPs and more!

  • EMBL – Nucleic acid, protein, structure, microarray data and more.

  • DBJJ – Nucleic acid, protein.

  • SwissProt – Very well annotated protein database.

  • Many other general and specialized databases exist.

Sequences databases ncbi genebank

Sequences DatabasesNCBI/Genebank

  • Nation Center for Biotechnology Information (NCBI)

  • Sponsored and run by the US government.

  • Contains many different databases and huge amounts of information.

  • Most or all data is freely downloadable.

  • This one site is probably sufficient for all your Nucleic acid a protein database needs!

Sequences databases entrez

Sequences DatabasesEntrez

  • Allows searching and access to NCBI databases.

Sequences databases sequence records

Sequences DatabasesSequence Records

  • LOCUS NumberSizeTypeTopology DivisionDate

  • DEFINITION - Name of the Sequence

  • ACCESSION - Unique Id number

  • VERSION - Other numbers which are associated


  • SOURCE – What was it isolated from

  • ORGANISM - More taxonomic detail

  • REFERENCE - Paper or papers about the sequence


    • TITLE


  • FEATURES - A complete list of all of the features of a sequence. Can be very extensive and useful!

  • ORIGIN – The actual Sequence!


Hands on

Hands on

  • Find a gene of interest using the Entrez interface.

  • We will be working with this sequence throughout class, so you may want to open a word processing program and save the sequence (only) there for future reference

General utilities

General Utilities


    • Translation

    • Restriction Digestion

    • Reformatting (alternately FASTA Formatter)

    • Complement/Reverse

    • Etc.


    • Melting Temperature of an oligo.

Hands on1

Hands on

  • Translate your sequence in all 6 reading frames.



  • Basic Local Alignment Search Tool

  • Compares a query sequences against all sequences in a database.

  • Very powerful for finding biologically significant relationships and full gene sequences in the database when you have a fragment etc.

  • Different types:

    • Nucleic acid – Nucleic Acid

    • Protein- Protein

    • Nucleic Acid Translation – Protein

    • Protein – Nucleic Acid Translation

    • Translation - Translation





Hands on2

Hands on

  • Use ~120 bases (2 lines) from your sequence to find at least two other sequences related to it.

  • Note that if we all hit NCBI BLAST at once, it will be slow. We may not have time to wait.

  • Get all 3 sequences (your original and two others) into FASTA format using READSEQ.

Multiple sequence alignment

Multiple Sequence Alignment

  • Many programs can align multiple sequences with each other to find the best fit for all.

  • This is generally more biologically meaningful for protein sequences since they are more highly conserved.

  • Clustal is the most common.

Multiple sequence alignment1

Multiple Sequence Alignment


  • LK PLSLERLFQ LK.PLSLERLFQ ......L..... lk plsLerlfq

Hands on3

Hands on

  • Use your FASAT Formatted sequences to perform a multiple sequence alignment.

  • Transfer the alignment to a word processing program and see if you can make it look decent.

  • Change to Courier or Courier New

  • Reduce Font Size

  • Change to Landscape view

Pcr primer design

PCR Primer Design

  • There are many PCR primer design programs online and off.

  • I recommend Primer 3. It is complex, but powerful.

  • You can ignore most parameters.

Hands on4

Hands on

  • Design primers for the sequence you have been working with.



  • Report:Please turn in a report which includes the following:

  • Information about your initial sequence including:

    • Genebank Accession Number

    • Species

    • Description

    • Location of ORF and any other important features.

  • Information about the 4 other sequences including the above

    • Genebank Accession Number

    • Species

    • Description

    • Location of ORF and any other important features.

    • E value from your BLAST results.

  • The sequences of the PCR primers you chose or a short explanation of why you could not find primers to amplify all of these genes.

  • The multiple sequence alignment with the locations of the primers clearly marked.

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