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Authors: Bruno Gaeta 


Similarity searching, multiple sequence alignment and protein families - undergraduate lab

Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...

Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching

Similarity searching, multiple sequence alignment and protein families - undergraduate lab https://tess.elixir-europe.org/materials/similarity-searching-multiple-sequence-alignment-and-protein-families-undergraduate-lab Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of the exercises make use of public databases they need to be checked and in some cases updated every time the lab is run. The lab is meant to be easily assessed using an online quiz (I use moodle). I provides a hands on introduction to NCBI BLAST, Interproscan, Clustal, MUSCLE and T-COFFEE, and HMMER.  Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Multiple sequence alignment and phylogeny - undergraduate lab

This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab...

Keywords: Clustalw, Multiple sequence alignment, Phylip, Phylogeny

Multiple sequence alignment and phylogeny - undergraduate lab https://tess.elixir-europe.org/materials/multiple-sequence-alignment-and-phylogeny-undergraduate-lab This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab environment - including some not so current programs (clustalw, treetool, seaview, phylip) as that's what we have installed at the moment and they're stable, but the content can easily be adapted to other environments and programs. The lab is meant to be easily assessed and I get the students to answer the question in a moodle quiz which makes marking easier. The lab follows some lectures on multiple sequence alignment and molecular phylogeny. Clustalw, Multiple sequence alignment, Phylip, Phylogeny biology and bioinformatics sophomore undergraduates 2013-11-12 2017-10-09
Sequence comparison - undergraduate lab

This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...

Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment

Sequence comparison - undergraduate lab https://tess.elixir-europe.org/materials/sequence-comparison-undergraduate-lab This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of the lab should be easy to adapt to other environments. This lab makes use of EMBOSS programs, prss in the FASTA package, as well as the NCBI BLAST website. I usually deliver this lab after a series of lectures discussing dotmatrix plots and sequence alignment. Students enter their answers to the questions into a quiz set up within moodle which allows for easier marking. Dotmatrix plots, Scoring matrices, Sequence alignment Undergraduate students 2013-11-12 2017-10-09