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Proteins and Enzymes- Emily > Bioinformatics > Flashcards

Bioinformatics Flashcards

1
Q

What are some of the uses of bioinformatics?

A
  • next generation sequencing
  • gene expression analysis
  • microarrays
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2
Q

What is sequence identity?

A

A perfect match between an unknown sequence and a known sequence.

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3
Q

What is sequence homology?

A

A partial match between an unknown sequence and a known sequence.

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4
Q

Give 3 protein sequence databases. Do they have cross collaboration?

A

UniProtKB, UniProtKB/TrEMBL and RefSeqP - no cross collarboration.

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5
Q

Give 3 DNA sequence databases. Do they have cross collaboration?

A

ENA/EMBL, Genbank and DDBJ- cross collaboration.

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6
Q

What does Ensembl do?

A

Provides annotations of numerous genomes, including their protein products.

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7
Q

What is a pairwise sequence alignment?

A

All possible alignments between two sequences are checked for sequence homology.

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8
Q

What is a global alignment used for?

A

Looking for homology between the same protein from different species.

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9
Q

What is a local alignment used for?

A

To match cDNA to genomic DNA.

To align two different protein sequences that share a common domain.

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10
Q

What is a global alignment?

A

Aligns the length of two sequences. Any homologous sequences can be aligned globally as long as they are similar enough.

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11
Q

What is a local alignment?

A

Alignment of two sequences such that homologous subsequences are aligned in between regions of non-related and unaligned sequences.

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12
Q

Why would gaps be introduced?

A

In order to produce the best possible global alignment.

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13
Q

What is the fasta format?

A

Most commonly used format for sequences.

> followed by a description of the sequence and its accession number

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14
Q

What is queried by blastn and in which database?

A

Nucleotide query, nucleotide database.

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15
Q

What is queried by blastp and in which database?

A

Amino acid query, amino acid database.

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16
Q

What is queried by tblastn and in which database?

A

Amino acid query, translated nucleotide database.

17
Q

What is queried by blastx and in which database?

A

Translated nucleotide query, amino acid database.

18
Q

What is queried by tblastx and in which database?

A

Translated nucleotide query, translated nucleotide database.

19
Q

Which BLAST searches are protein searches?

A

Blastp and blastx.

20
Q

What is the score?

A

Calculated by increasing the score for matches/similarities and decreasing for mismatches/gaps.

21
Q

What are identities?

A

The number of residues that are identical in the alignment.

22
Q

What are positives?

A

The number of similar residues in the alignment.

23
Q

What does gaps mean in a BLAST output?

A

The number of gaps in the alignment.

24
Q

What is the E (expect) value?

A

A measure of how reliable the alignment is.

25
Q

How can sequences be considered homologous?

A

> 25% identity in amino acids sequence or >75% identity in nucleotide sequence, for sequences larger than 100 amino acids.

26
Q

What is Clustal?

A

A multiple sequence alignment program.

27
Q

What is considered a good alignment?

A
  • at least 10-30 residues long
  • have at least 1-3 stars
  • have 5-7 colons
  • have a few periods
28
Q

What does * represent in a Clustal output?

A

An entirely conserved column.

29
Q

What does : represent in a Clustal output?

A

A column where all of the residues have roughly the same size and hydrophobicity.

30
Q

What does . represent in a Clustal output?

A

A column where the size and hydrophobicity has been conserved over the course of evolution.

31
Q

Why are multiple sequence alignments more informative than pairwise alignments?

A

They have a lower % identity.

32
Q

What does a phylogenetic tree show?

A

The evolutionary relationship between species or sequences.

Proteins and Enzymes- Emily (14 decks)

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