H3ABioNet

Pan African Bioinformatics Network for H3Africa

Working with the Human Genome Sequence - Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi 26-30 January 2015

This 5-day Workshop provides an intensive introduction to bioinformatics tools freely available on the internet, focusing primarily on the Human Genome data. Students will be given hands-on training in the use of public databases and web-based sequence analysis tools. All course materials will be provided and also made available on the Web. The course has a strong emphasis on applied training, and practical exercises along with interaction and discussion between students and instructors are key features of the programme. Each student will have access to a desktop PC for the duration of the course.

This course is limited to 20 participants from African institutes. Please visit the application page for online registration. There is no course fee for applicants from non-commercial institutes.

A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee. The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750.

  • Pre-requisites - The workshop is open to research scientists based in institutes anywhere in Africa (including laboratory and clinical staff as well as specialists in related fields). Applicants should have a minimum of a degree in a biological discipline.
  • Cost - There is no course fee for applicants from non-commercial institutes. Bursaries are available for travel and accommodation, these are subject to a selection process and are awarded by merit. Applicants may apply for a bursary during the online application process. Please visit Bursaries for Wellcome Trust Advanced Courses for more information.
  • Applications - Applicants will be required to complete an online application form together with a 250-word outline of the relevance of the course to their work. Please note that documentation supporting the application will be required from the applicant's Supervisor/Head of Department.

Closing date for application is 26 September 2014. Applications will not be accepted after this date. Successful applicants will be notified as soon as possible.

Any queries should be sent to This email address is being protected from spambots. You need JavaScript enabled to view it.

The workshop will cover the following topics:

Sequence Formats and Retrieval:

  • DNA databases: Embl, Genbank, DDBJT
  • Protein databases: Uniprot
  • Entrez - seach sequence information, including Refseq
  • BLAST

Genome Browsing:

  • Ensembl - full coverage including BioMart
  • VEGA
  • UCSC

De novo analysis of Sequence:

  • VEGA
  • DNA analysis - ORF finder
  • Alignment of splicing cDNA to genomic DNA - Splign, Est2genome, SIM4
  • Multiple Sequence Alignment - MUSCLE, CLUSTALW
  • Alignment viewing and Editing- Jalview, GeneDoc

Exploring Function and Disease:

  • Understanding Protein Function - from domains to structure (covering Pfam, InterPro, PDB)
  • Secondary Structure predictions
  • Disease databases COSMIC, OMIM, DECIPHER
  • Mapping disease associated SNPs to Proteins - Polyphen, SNPs 3D Rfam and microRNAs (miRBase)

Sequence Variation:

  • Ensembl SNP information, Geneview in dbSNP
  • Genotyping
  • Haplotypes and HapMap
  • Haploview

Comparative Sequence Analysis:

  • Homologous gene identification - Paralogues and Orthologues
  • Ensembl - orthologue prediction, MultiContigView
  • EntrezGene - BLink, Homologene
  • Comparative Genome Analysis - UCSC, Zpicture, ECR browserVISTA

The original workshop call can be found here.