100% de satisfacción garantizada Inmediatamente disponible después del pago Tanto en línea como en PDF No estas atado a nada
logo-home
Buscado previamente por ti
Buscado previamente por ti
logo
Bio-informatica samenvatting/hulpbestand voor examen 16,66 €
Añadir al carrito
Navegar rápidamente a
Vista previa
  2.  
  3. Katholieke Universiteit Leuven (KU Leuven)
  4.  
  5. Biomedische Wetenschappen
  6.  
  7. Bio-informatica

Resumen

Bio-informatica samenvatting/hulpbestand voor examen
 1 veces vendidas
  • Grado
  • Bio-informatica
  • Institución
  • Katholieke Universiteit Leuven (KU Leuven)

Samenvatting van slides+notities van bio-informatica. Codes met uitleg en werkzittingen uitwegewerk+uitleg. Uitleg van verschillende databases en veel gebruikte codes.

Vista previa 4 fuera de 33  páginas

Información del documento

  • 26 de mayo de 2024
  • 33
  • 2023/2024
  • Resumen

Temas

  • hulpbestand examen
  • bioinformatica
  • cpg
  • werkzittingen
  • code
  • python
  • jupyter
  • bash

Escuela, estudio y materia

  • Katholieke Universiteit Leuven (KU Leuven)
  • Biomedische Wetenschappen
  • Bio-informatica
Todos documentos para esta materia (21)

Vendedor

avatar-seller
sisivorst

Vista previa del contenido

Bioinformatica
Inhoud
Les 1: intro+ databases ............................................................................................................2
Gendatabase ............................................................................................................................2
Protein database ...................................................................................................................3
Les 2: databases ......................................................................................................................4
Ontologies ............................................................................................................................4
Gene expression ....................................................................................................................5
Phenotypes/Diseases..............................................................................................................6
Model Organism databases ....................................................................................................6
Les 3: genome browsers+ SQL .................................................................................................6
Genome browsers .....................................................................................................................6
Homology.............................................................................................................................7
Database architectures...........................................................................................................8
Les 4: Linux + Jupyter .......................................................................................................... 10
Navigating the file system ..................................................................................................... 10
Additional Jupyternotebooks notes ........................................................................................ 13
Les 5: EMBOSS + BedTools exercises .................................................................................... 14
Les 6: Gene prediction ........................................................................................................... 15
Les 7+8: Python .................................................................................................................... 17
Les 9: Alignment, pattern matching, gene set analysis ............................................................. 19
Werkzitting1 ......................................................................................................................... 25
Information retrieval............................................................................................................ 25
CpG islands ........................................................................................................................ 26
Unknown sequence study...................................................................................................... 28
Werkzitting 2 ........................................................................................................................ 30
Python CpG island .............................................................................................................. 30
miRNA ............................................................................................................................... 32

,Les 1: intro+ databases




Gendatabase
- Entrez gene
o Onderdeel van NCBI: https://www.ncbi.nlm.nih.gov/gene/
o Each line is a transcript isoform (due to alternative promoters, and alternative
splicing); look at the exons, introns, non-coding exons (light greens: 5’UTR,
3’UTR), coding exons (dark green)
o Each transcript has a unique NM_ identifier = RefSeq identifier
o Each NM transcript corresponds to a unique NP_ protein entry
o More details about each NM/NP and links to the sequence in Entrez
Nucleotide are at the bottom of the Gene page
▪ Entrez Nucleotide contains all nucleotide sequences
▪ Search Nucleotide db with NM_000564
▪ (After the dot “.” is the version number)
- Refseq
o https://www.ncbi.nlm.nih.gov/refseq/
o Many sequences were/are represented more than once in GenBank
o RefSeq = curated “secondary” database that aims to provide a
comprehensive, integrated, nonredundant set of sequences
o Goal is to provide a reference sequence for each molecule in the central dogma
(DNA, mRNA, and protein)
o Each RefSeq represents a single, naturally occurring molecule from one
organism
o Nucleotide and protein sequences in RefSeq are explicitly linked to one
another
o Distinct accession number: 2+6 format (2 letters, underscore, six-digit number)
▪ NT_123456 (Genomic contigs), NM_123456 (mRNAs), NP_123456
(Proteins)
▪ XM_123456 (Model mRNAs), XP_123456 (model proteins):
computational predictions

,To visualize the data, download GenBank format (.gb) as textfile and open it in text editor,
such as Visual Studio Code or Jupyternotebooks.
- How to download:
o Click on “Send to” (right upper screen)
o Select “Complete Record” and “File”
o Choose GenBank format or FASTA (no header and features)
- In feature
o Sequence has a coding sequence (CDS) made up of five exons
▪ First exon begins at base 201 and ends at base 224
▪ Then is joined at basepair 1550 until bp 1920, and so forth.
o Each comma in this line represents a splicing event, and each “..” represents
the string of letters between the two coordinates.
o The gene product is eukaryotic initiation factor 4E-II, and the gene name is
eIF4E




EMBL/EBI
o https://www.ebi.ac.uk/
o European database
o DBFETCH provides an easy way to retrieve entries from various databases at
the EMBL-EBI
o Format:https://www.ebi.ac.uk/Tools/dbfetch/db=refseqn;id=NM_000231;form
at=fasta&style=raw
Protein database
- Uniprot: https://www.uniprot.org/
o Gives general feature format (GFF) (text file)
▪ Click download
▪ Choose GFF format
- Protein sequences in databases can be derived from translation of nucleotide
sequences (secondary databases)
o e.g., RefSeq NM_ to RefSeq NP_
o e.g.,TrEMBL
o Go to the protein database, following one of the NP_isoforms
- There are also curated databases: experts enhance the original data by adding new
information

, o e.g., SwissProt (in the UniProt knowledgebase)
▪ Information from literature
▪ Curator-evaluated computational analysis/predictions
- 3D structures
o https://www.ncbi.nlm.nih.gov/structure/ or Uniprot→ structure


Les 2: databases




Ontologies
- Gene ontology (GO)
o https://geneontology.org/ or https://www.ebi.ac.uk/QuickGO/ (human usually
capitalized)
▪ Data downloaden QuickGo
• Click on export
• Choose format: gen association file (then add .txt in the name)
• Adjust the amount of annotations
o Specific purpose: “Annotation of genes and proteins in genomic and protein
databases”
o Facilitate complex queries
o Applicable to all species
o Databases involved:
▪ FlyBase (Drosophila)
▪ MGI (Mouse)
▪ SGD (S. cerevisae)
▪ TAIR (Arabadopsis)
▪ TIGR (microbes including prokaryotes)
▪ SWISS-PROT (several thousand species inc. human)
▪ PSU (P. falciparum)
▪ ZFIN (zebrafish)
▪ PAMGO (plant pathogens)
o GO structure

Los beneficios de comprar resúmenes en Stuvia estan en línea:

Garantiza la calidad de los comentarios

Garantiza la calidad de los comentarios

Compradores de Stuvia evaluaron más de 700.000 resúmenes. Así estas seguro que compras los mejores documentos!

Compra fácil y rápido

Compra fácil y rápido

Puedes pagar rápidamente y en una vez con iDeal, tarjeta de crédito o con tu crédito de Stuvia. Sin tener que hacerte miembro.

Enfócate en lo más importante

Enfócate en lo más importante

Tus compañeros escriben los resúmenes. Por eso tienes la seguridad que tienes un resumen actual y confiable. Así llegas a la conclusión rapidamente!

Preguntas frecuentes

What do I get when I buy this document?

You get a PDF, available immediately after your purchase. The purchased document is accessible anytime, anywhere and indefinitely through your profile.

100% de satisfacción garantizada: ¿Cómo funciona?

Nuestra garantía de satisfacción le asegura que siempre encontrará un documento de estudio a tu medida. Tu rellenas un formulario y nuestro equipo de atención al cliente se encarga del resto.

Who am I buying this summary from?

Stuvia is a marketplace, so you are not buying this document from us, but from seller sisivorst. Stuvia facilitates payment to the seller.

Will I be stuck with a subscription?

No, you only buy this summary for 16,66 €. You're not tied to anything after your purchase.

Can Stuvia be trusted?

4.6 stars on Google & Trustpilot (+1000 reviews)

45,681 summaries were sold in the last 30 days

Founded in 2010, the go-to place to buy summaries for 15 years now

Empieza a vender

Vistos recientemente

Lote ·

(0)

2023 ATI MATERNAL NEWBORN PROCTORED RETAKE EXAM A

Examen ·

(0)

Crossfit Level 1 – deutsch 2025 Exam Questions With Answers New Update

Examen ·

(2)

Chemistry Atoms First 2nd Edition Flowers Test Bank

Examen ·

(1)

WSET Level 2 Exam Questions with Correct Answers 2023/2024

Examen ·

(0)

ATI RN Fundamentals Online Practice Assessment A 2023/2024

Resumen ·

(67)

Uitgebreide samenvatting approaches to psychology H1 tm 10

Examen ·

(1)

Nurs 5315 UTA exam 1 questions with correct answers

Notas de lectura ·

(0)

All Lectures of Philosophy Of Administration Studies 20/21

Notas de lectura ·

(0)

Hoorcolleges + aantekeningen Mind, Brain and Education

16,66 €  1x  vendido
  • (0)
Añadir al carrito
Añadido