7. Sequence analysis

Which statements regarding sequence similarities are correct?

1) If two sequences are 60% identical, they are also 60% homologous -> wrong; sequence similarity is quantitative and being homologous is qualitativ (yes or no)

2) Two paralogous sequences are also two homologous sequences -> correct

3) 1 to 1 orthologous genes are often assumed to have the same function -> correct

4) If a duplication of Gene G occured on the lineage to species A after the split of species A and B, species A has two paralogs of gene G and these two be orthologues of G in species B -> correct

5) if two sequences in two species are reciprocal best hits they are usually defined as paralogs -> wrong, this is the defintion/ identification of orthologs

A global alignment is...

1) An alignment of two genomes -> wrong, of two sequences

2) A sequence alignment with more than two species -> wrong

3) A sequence alignment along the entire length of the compared sequences -> correct

4) A sequence alignment of a subset of two sequences -> wrong

5) A heursitic search algorithm -> wrong

Which statement are correct for scoring matrices for alignments?

1) A scoring matrix is a mathematically proven algorithm -> wrong, not an algorithm, just a matrix (would be correct for Smith-Waterman / Needleman-Wunsch algorithm)

2) If all mismatches in a scoring matrix are scored equally, one assumes that all nucleotides or amino acids have the same frequency in the alignment

3) A global alignment is independent of the scoring matrix -> wrong, you cannot do an alignment without a scoring matrix

4) The Smith-Waterman alignment finds the optimal alignment independent of the scoring matrix -> wrong, dependent of the scoring matrix

5) One can run Blast with and without a scoring Matrix -> wrong does an alignment which needs a scoring matrix

Which statements regarding the BLAST algorithm are true?

1) BLAST uses the needleman-Wunsch algorithm -> wrong; with Needleman-Wunsch it would take too long/expensive; it also doesnt use Smith-Waterman

2) BLAST can only be used to align protein sequences -> wrong, also DNA sequences

3) BLAST is a global alignment algorithm -> wrong, its a local alignment algorithm

4) BLAST is a heuristic, i.e. it does not guarantee to find the best alignment -> correct

5) BLAST does not use scoring matrices and hence is faster than optimal alignment algorithms -> wrong, uses scoring matrices

If you set k=3 for the query sequence "AWKLTSVCAGQL", how many words has the k-letter word list of blast?

1) Depends on the scoring matrix

2) 3

3) 4

4) 9

5) 10 -> correct

Which statement regarding mapping of short reads is true?

1) BLAT was invented to map the billions of reads generated by NGS seqencers -> wrong, for HGP; its too slow for NGS data

2) Mapping of short reads requires alignments optimized for sensitivity -> wrong; not more sensitive and more speed at a time; actually the opposite is true. So for short reads someone needs more speed

3) BWA and Bowtie are two commonly used mappers of NGS data -> correct

4) BLASTN is commonly used to map NGS reads -> wrong; not at all used for mapping NGS reads (not the right tool)

5) Burrow-Wheeler transformation is an algorithm that speeds up mapping by allowing the reference genome to be more compressed -> correct