# Datalab 5: Group 1 Session

Let’s keep things centralized! Easier to go back to later!

This is the link to this page: https://hackmd.io/@yinhsieh/S1-L2YFH_
Today’s Schedule

- [x] 14.15 - 14.25 : Setup & How To
- [x] 14.25 - 14.30 : Comments from Homework 4
- [x] 14.30 - 15.10 : Overview of Review Topics
- [x] 15.10 - 15.25 : Break
- [x] 15.25 - 15.45 : Finish Overview of Review Topics
- [x] 15.45 - 16.15 : Start on Homework 5
- [x] 16.15-17.00 : Homework 5

## Breakout Room Assignment
When we start on the homework, you can choose which breakout room you want to be in. Please write yourself under one of the rooms. You can also work alone, then just stay in the main meeting room.

When you have a question while in a breakout room, write it under the room assignment (otherwise if I am in another breakout room I cannot see it).

If you have a question in the main meeting room, just write it under the **Questions** section below.

I will do my best to respond to questions asap ;-)

- Room 1

- Room 2

- Room 3
- Per-Aksel W.M
- Terese Vollstad
- Nina
-

- Room 4
- Helene & Thea Ramona
- Anne
- Ásla
- Ragnhild

- Room 5
- Ida Amalie
- Asgeir
- Kathleen
- Kristin

## Questions

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type them here

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## Brief Review of Previous Datalabs/Homework

Everything below matches the slides I show in the Zoom, with the links.

### Homework 1: Intro to Biological Sequences

*Concepts*

- DNA vs. RNA vs protein +
- DNA transcription (DNA → RNA)
- DNA translation (DNA → RNA → protein)

- Sequence similarity probabilities ++
- Mutation rate calculations ++

*New Tools*

- Expasy Translate tool (6-frame translation of DNA or RNA sequences)
- https://web.expasy.org/translate/

### Homework 2: Sequence alignment and biological databases

*Concepts*

- sequence similarity search in databases (via Blast)
- protein information search in UniProt ++
- protein structure search in the PDB++

- likelihood of finding sequence in database and hit significance (e-value) ++
- local vs. global sequence alignment ++

*New Tools*

- NCBI (super)database
- https://www.ncbi.nlm.nih.gov/
- BLAST database querying
- https://blast.ncbi.nlm.nih.gov/Blast.cgi
- UniProt standardised protein database
- https://www.uniprot.org/
- PDB structural database
- https://www.rcsb.org/

### Homework 3: Multiple sequence alignments (MSA)

*Concepts*

- from biological question to bioinformatic analysis +
- extracting sequences for various organisms

- making multiple sequence alignments +
- reading and interpreting multiple sequence alignments +
- remapping of MSA positions to protein structure +

*New Tools*

- KEGG pathway database for enzyme function
- https://www.genome.jp/kegg/
- ClustalOmega aligner
- https://www.ebi.ac.uk/Tools/msa/clustalo/

### Homework 4: More BLAST, peptide mass, and alignments

*Concepts*

- species identification
- how to use BLAST to identify sequences + certainty +

- mass spectrometry++
- using peptide masses to find modified amino acids ++

- recap of conservation: coverage vs percentage identity +

*New Tools*

- Expasy peptide mass tool
- https://web.expasy.org/peptide_mass/