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‎.vscode/settings.json‎

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‎Pipfile.lock‎

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‎docs/blast/blast_online.md‎

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# Using Blast online
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Blast is one of the most used bioinformatics tools ever written.
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It allows to find similaroties between sequences of proteins or nucleotides, at a reasonable speed.!
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Its ancestor, the fasta suite (like the format) used an algorithm clled smith-waterman.
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While very accurate, was very slow.
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Blast is available opnline on the ncbi website at the following address <https://blast.ncbi.nlm.nih.gov/Blast.cgi>
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Let us try it out!
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### Your first blast
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go on the blast ncbi website and select protein blast
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![](../img/blast_0.png)
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Copy and paste the following protein sequence
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```bash
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>a_protein
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MKWVTLISFIFLFSSATSRNLQRFARDAEHKSEIAHRYNDLKEETFKAVAMITFAQYLQR
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CSYEGLSKLVKDVVDLAQKCVANEDAPECSKPLPSIILDEICQVEKLRDSYGAMADCCSK
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ADPERNECFLSFKVSQPDFVQPYQRPASDVICQEYQDNRVSFLGHFIYSVARRHPFLYAP
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AILSFAVDFEHALQSCCKESDVGACLDTKEIVMREKAKGVSVKQQYFCGILKQFGDRVFQ
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ARQLIYLSQKYPKAPFSEVSKFVHDSIGVHKECCEGDMVECMDDMARMMSNLCSQQDVFS
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GKIKDCCEKPIVERSQCIMEAEFDEKPADLPSLVEKYIEDKEVCKSFEAGHDAFMAEFVY
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EYSRRHPEFSIQLIMRIAKGYESLLEKCCKTDNPAECYANAQEQLNQHIKETQDVVKTNC
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DLLHDHGEADFLKSILIRYTKKMPQVPTDLLLETGKKMTTIGTKCCQLGEDRRMACSEGY
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LSIVIHDTCRKQETTPINDNVSQCCSQLYANRRPCFTAMGVDTKYVPPPFNPDMFSFDEK
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LCSAPAEEREVGQMKLLINLIKRKPQMTEEQIKTIADGFTAMVDKCCKQSDINTCFGEEG
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ANLIVQSRATLGIGA
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```
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into the "enter query sequence" form
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![](../img/blast_1.png)
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and click "Blast" (you may have to scroll down a bit)
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![](../img/blast_2.png)
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then wait for your results.
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Once the results have loaded, scroll down to the first hit.
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!!! question
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From which organism is our protein? What is it?
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![](../img/blast_3.png)
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!!! note
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Sometyimes, two hits have an identical score. In that case, be careful with the interpretation.
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### Restrict the search parameters
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Let us imagine we'd like to compare our query to only human proteins.
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We can select an organism to restrict our search.
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![](../img/blast_4.png)
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!!! question
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What is the percentage identidy between the chicken and human albumin?
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!!! question
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Here is an unknown protein. From which organism and which function does it have?
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`MVLSAADKGNVKAAWGKVGGHAAEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHG`
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`AKVAAALTKAVEHLDDLPGALSELSDLHAHKLRVDPVNFKLLSHSLLVTLASHLPSDFTP`
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`AVHASLDKFLANVSTVLTSKYR`

‎docs/img/blast_0.png‎

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‎docs/img/blast_1.png‎

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‎docs/img/blast_2.png‎

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‎docs/img/blast_3.png‎

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‎docs/img/blast_4.png‎

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‎docs/index.md‎

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This website is a collection of lectures and tutorials given during the annual Bioinformatics course given at [SLU](https://www.slu.se) by the [SGBC](http://sgbc.slu.se).
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## Course information
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- What: Bioinformatics, 15 ECTS
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- Where: SLU, Campus Ultuna, Uppsala, Sweden
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- When: 21 Jan - 25 March 2019
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- Course page: [link](https://www.slu.se/en/education/programmes-courses/courses/?sprak=en&anmkod=30181.1819)
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Welcome to the course!
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## Table of Content
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* Week 1
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* [Introduction to proteins analysis](proteins)
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* Week 2
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* [Introduction to the command-line](unix)
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* [Cloud Computing](cloud)
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* [Installing Software](software)
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* [Version control with Git](git)
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* [Command-line Blast](blast)
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* [Project organisation](project_organisation)
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* Week 3
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* [Sequencing Technologies](seq_tech)
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* [Quality Control](tutorials/docs/qc.md)
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* [De-novo Genome Assembly](tutorials/docs/assembly.md)
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* [Assembly Challenge](assembly_challenge)
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* [Genome Annotation](tutorials/docs/annotation.md)
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* [Pan-genome Analysis](tutorials/docs/pan_genome.md)
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* [Nanopore Sequencing](tutorials/docs/nanopore.md)
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* Week 4
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* [RNA Sequencing](tutorials/docs/rna.md)
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* [Metabarcoding](tutorials/docs/16S.md)
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* [Metagenome assembly](tutorials/docs/meta_assembly.md)
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* [Comparative metagenomics](tutorials/docs/wms.md)
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* Week 5
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* [Genome Annotation (NBIS)](nbis_annotation/schedule.md)
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### Week 1
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- [Online Blast](blast/blast_online)
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- [Introduction to proteins analysis](proteins)
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### Week 2
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- [Introduction to the command-line](unix)
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- [Cloud Computing](cloud)
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- [Installing Software](software)
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- [Version control with Git](git)
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- [Command-line Blast](blast)
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- [Project organisation](project_organisation)
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### Week 3
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- [Sequencing Technologies](seq_tech)
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- [Quality Control](tutorials/docs/qc.md)
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- [De-novo Genome Assembly](tutorials/docs/assembly.md)
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- [Assembly Challenge](assembly_challenge)
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- [Genome Annotation](tutorials/docs/annotation.md)
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- [Pan-genome Analysis](tutorials/docs/pan_genome.md)
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- [Nanopore Sequencing](tutorials/docs/nanopore.md)
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### Week 4
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- [RNA Sequencing](tutorials/docs/rna.md)
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- [Metabarcoding](tutorials/docs/16S.md)
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- [Metagenome assembly](tutorials/docs/meta_assembly.md)
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- [Comparative metagenomics](tutorials/docs/wms.md)
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### Week 5
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- [Genome Annotation (NBIS)](nbis_annotation/schedule.md)
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## License
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The following people have contributed to these course material, in no particular order:
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* [Hadrien Gourlé](https://github.com/HadrienG)
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* [Juliette Hayer](https://github.com/jhayer)
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* [Oskar Karlsson](https://github.com/Ackia)
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* [Jacques Dainat](https://github.com/NBISweden)
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- [Hadrien Gourlé](https://github.com/HadrienG)
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- [Juliette Hayer](https://github.com/jhayer)
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- [Oskar Karlsson](https://github.com/Ackia)
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- [Jacques Dainat](https://github.com/NBISweden)

‎mkdocs.yml‎

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site_name: Bioinformatics course
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theme:
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name: cinder
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name: cinder
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pages:
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- Home: index.md
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- Week 1:
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- Proteins: proteins.md
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- Week 2:
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- Unix: unix.md
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- Cloud Computing: cloud.md
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- Installing Software: software.md
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- Git: git.md
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- Command-line Blast: blast.md
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- Project Organisation: project_organisation.md
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- Week 3:
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- Sequencing Technologies: seq_tech.md
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- Quality Control: tutorials/docs/qc.md
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- Assembly Challenge: assembly_challenge.md
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- De-novo Genome Assembly: tutorials/docs/assembly.md
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- Genome Annotation: tutorials/docs/annotation.md
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- Pan-genome Analysis: tutorials/docs/pan_genome.md
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- Nanopore Sequencing: tutorials/docs/nanopore.md
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- Week 4:
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- RNA Sequencing : tutorials/docs/rna.md
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- Metabarcoding: tutorials/docs/16S.md
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- Metagenome assembly: tutorials/docs/meta_assembly.md
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- Comparative metagenomics: tutorials/docs/wms.md
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- Week 5 - Eukaryotic Annotation:
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- Schedule: nbis_annotation/schedule.md
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- Practical 1: nbis_annotation/practical_session/practical1.md
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- Practical 2: nbis_annotation/practical_session/practical2.md
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- Practical 3: nbis_annotation/practical_session/practical3_manualCuration.md
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- Practical 4: nbis_annotation/practical_session/practical4_funcAnnotInterp.md
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- Extras:
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- WebApollo: nbis_annotation/practical_session/UsingWebApollo.md
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- Protein, EST and RNA-seq data: nbis_annotation/practical_session/practical2_sub_gatherEvidence.md
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- Assembling transcripts: nbis_annotation/practical_session/practical2_sub_transcriptome.md
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- Evidence Based Annotation: nbis_annotation/practical_session/practical2_sub_makerNoAbinit.md
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- Abinitio Annotation: nbis_annotation/practical_session/practical2_sub_makerAbinit.md
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- Comparing Annotations: nbis_annotation/practical_session/practical2_sub_makerCompareAnnot.md
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- Configuring Maker (I): nbis_annotation/practical_session/practical2_supl_maker.md
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- Configuring Maker (I): nbis_annotation/practical_session/practical2_supl3_maker.md
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- Inspecting Maker output: nbis_annotation/practical_session/practical2_supl2_maker.md
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nav:
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- Home: index.md
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- Week 1:
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- Blast Online: blast/blast_online.md
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- Proteins: proteins.md
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- Week 2:
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- Unix: unix.md
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- Cloud Computing: cloud.md
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- Installing Software: software.md
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- Git: git.md
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- Command-line Blast: blast.md
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- Project Organisation: project_organisation.md
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- Week 3:
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- Sequencing Technologies: seq_tech.md
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- Quality Control: tutorials/docs/qc.md
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- Assembly Challenge: assembly_challenge.md
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- De-novo Genome Assembly: tutorials/docs/assembly.md
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- Genome Annotation: tutorials/docs/annotation.md
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- Pan-genome Analysis: tutorials/docs/pan_genome.md
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- Nanopore Sequencing: tutorials/docs/nanopore.md
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- Week 4:
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- RNA Sequencing: tutorials/docs/rna.md
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- Metabarcoding: tutorials/docs/16S.md
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- Metagenome assembly: tutorials/docs/meta_assembly.md
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- Comparative metagenomics: tutorials/docs/wms.md
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- Week 5 - Eukaryotic Annotation:
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- Schedule: nbis_annotation/schedule.md
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- Practical 1: nbis_annotation/practical_session/practical1.md
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- Practical 2: nbis_annotation/practical_session/practical2.md
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- Practical 3: nbis_annotation/practical_session/practical3_manualCuration.md
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- Practical 4: nbis_annotation/practical_session/practical4_funcAnnotInterp.md
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- Extras:
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- WebApollo: nbis_annotation/practical_session/UsingWebApollo.md
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- Protein, EST and RNA-seq data: nbis_annotation/practical_session/practical2_sub_gatherEvidence.md
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- Assembling transcripts: nbis_annotation/practical_session/practical2_sub_transcriptome.md
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- Evidence Based Annotation: nbis_annotation/practical_session/practical2_sub_makerNoAbinit.md
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- Abinitio Annotation: nbis_annotation/practical_session/practical2_sub_makerAbinit.md
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- Comparing Annotations: nbis_annotation/practical_session/practical2_sub_makerCompareAnnot.md
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- Configuring Maker (I): nbis_annotation/practical_session/practical2_supl_maker.md
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- Configuring Maker (I): nbis_annotation/practical_session/practical2_supl3_maker.md
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- Inspecting Maker output: nbis_annotation/practical_session/practical2_supl2_maker.md
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markdown_extensions:
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extra_css:
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- css/admonition.css
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- css/navbar.css

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