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BINF511 EXAM STUDY GUIDE
What is a binary file? - Answer A file that is machine readable. It requires an interpreter to be human readable. What is the purpose of a README file? - Answer They are plain text files that give basic information about the directory or software. These are often used to ensure the user knows the purpose of the directory. They are especially useful in multiuser systems. Based on the given tree, what is the absolute path to phone numbers.txt - Answer /user 1/desktop/phone numbers.txt/ Based on the given tree, give the relative path from info.pdf to user 2 - Answer ../../../user 2/ What are the parts of this UNIX prompt: hugin:~stromvik% - Answer hugin: = computer name ~ = home directory stromvik = login username % = prompt (can be various systems %$>) what does the unix comand pwd do? - Answer prints the working directory what does the unix command ls do? - Answer prints a list of the contents of the working directory what does the unix command ls -l do? - Answer long list - it prints a list of the contents of the working directory with more details than the standard ls If a file had the permission 764 what would it mean? - Answer The owner can read, write and execute. The group can read and write. The world can read. what are the numerical values associated with the read, write and execute permissions?
- Answer read = 4 write = 2 execute = 1 in what order do the permissions occur? - Answer owner, group, world what does the unix command chmod do? - Answer allows you to change the file permissions what does the unix command cd do? - Answer allows the user to change the working directory (can use absolute or relative path)
what unix command will display the username? - Answer whoami what does the the unix command cp do? - Answer copies the specified file to the specified location what does the unix command mv do? - Answer 1. it can make a copy of the file if you choose a file name as the location
- it will move the specified file to the specified directory what unix command will make a new directory? - Answer mkdir what does the unix command rm do? - Answer removes the specified file how can you find what a unix command does? - Answer man (command) what is the unix shell? - Answer the interpreter for the unix commands. Commands can vary between different shells what is the standard in and standard out? - Answer standard in: the terminal where you tell the computer what to do by typing a command and pressing enter standard out: the terminal where the computer prints to the screen in response to a command. the standard out is used unless another location is specified. what does the unix command cat do? - Answer flashes the contents of the specified file to the standard out. what do the unix commands more and less do? - Answer allow you to page through the specified file. when using more or less, what are the keys to page down, page up, and quit? - Answer page down = space page up = b quit = q what does the unix command head do? - Answer shows the first part of the specified file. The number of lines shown can be specified using -# after. what does the unix command tail do? - Answer shows the last part of the specified file. The number of lines can be specified using -# after. what symbol is used to indicate that the contents of a file are to be used as the input in unix? - Answer < What is the difference between the > and >> in unix? - Answer > prints to the specified file and will overwrite the existing file if it already exists.
adds the output to the end of an existing file
how do you compress your file in unix? - Answer gzip. it will ad the extension .gz what does the unix command gunzip do? - Answer uncompresses the specified file. what is safe file transfer protocol (sftp)? - Answer it is an electronic way to transfer files between a local and remote computer. how to you establish a connection between two computers for a safe file transfer protocol? - Answer after the local computers prompt, type sftp and the name of the computer you are connecting to (usually your username on that computer@IPadress) What are the rules for file names using unix? - Answer you can use. and _. You can not use spaces or other special characters. what do the unix commands put and mput do when using safe file transfer protocol? - Answer put = moves 1 file from local machine to remote machine mput = moves multiple files from local machine to remote machine what do the unix commands get and mget do when using safe file transfer protocol? - Answer get = moves 1 file from the remote machine to the local machine mget = moves multiple files from the remote machine to the local machine What is the purpose of a loop in unix - Answer it allows you to automate a task that you want done to multiple files so you do not need to type the same commands repeatedly
what does the unix command echo do? - Answer it prints whatever is on the rest of the line is to the standard out.
how do you stop a loop in unix? - Answer type end as the last line
What does HTML stand for? - Answer Hypertext Markup Language
what is HTML used for? - Answer programming language to structure and format information for webpages
what is XML? - Answer Extensible Markup Language
what is XML used for? - Answer to write files that can be parsed easily. The goal is to
make 1 file type that multiple programs and databases can use standard tags and share information
what is ASN.1? - Answer Abstract syntax notation 1
what is ASN.1 used for? - Answer formal language to structure information to share between applications (similar to XML). Genbank is based on ASN.
what is the central dogma of molecular biology? - Answer DNA -> RNA -> Protein
What is the genome? - Answer A collection of all of the genes (DNA) within an organism.
what is the ORFome? - Answer A collection of all of the open reading frames (ORFs) in an organism.
What is the transcriptome? - Answer A collection of all of the transcripts (RNA) in an organism
What is the proteome? - Answer A collection of all of the gene products (proteins) in an organism
What is the metabolome? - Answer A collection of all of the metabolites in an organism
what does comparative genomics assess? - Answer Typically compares the genomes of 2 different organisms
what does functional genomics assess? - Answer Study's the function of genes. This will often include transcriptomics
what does structural genomics study? - Answer focuses on the physical structure and
adaptors and added to a flow cell. Clusters of DNA are formed via bridge amplification. At each base, a fluorescently labelled terminator is added and read. It is then removed so the next base can be called.
Describe the basics of Oxford Nanopore sequencing - Answer DNA molecule is pulled through a pore in the membrane. As the molecule moves through, the charge across the membrane changes allowing for base calling.
Describe the basics of Single molecule real time (SMRT) sequencing - Answer uses a zeromode wave guide: a compartment with only 1 polymerase and 1 DNA template. Fluorescent molecules are cleaved off if they are incorporated. This is detected and allows for base calling.
Describe the basics of 10x Genomics sequencing - Answer Microfluidics based methods of single cell sequencing. Uses barcoding to determine which molecule you are "on". I don't think they are doing this anymore.
What sequencing methods are considered next gen (2nd gen) - Answer Illumina, 454 pyrosequencing, Ion torrent
What sequencing methods are considered long read (3rd gen) - Answer Oxford Nanopore, Single molecule real time (SMRT), and 10x genomics
What is a genomic DNA library? - Answer a collection of all of the DNA in a organism.
What are 2 methods of whole genome sequencing - Answer Shotgun sequencing, Clone-contig approach
What are the steps of shotgun sequencing - Answer 1. fragment DNA into large pieces (2000kb)
- ends of clones are sequenced 3.contigs are assembled (made up of contiguous sequences based on overlap)
What are the steps of clone-contig approach sequencing - Answer 1. clones are screened and ordered
- sequence selected bacterial artificial chromosomes (BAC) clones (150-200kb)
- Fragments overlap because of partial digest
- chromosome walk by sequencing, then designing primers to that sequence, sequence, design new primers, and repeat
- Ordered sequenced clones are put together into a physical map
What is Expressed sequencing tags (EST) sequencing - Answer 1. Early version of transcriptomics (not used much anymore)
- cDNA clones are randomly selected and sequenced (typically uses sanger)
- usually only the 5' end is sequenced because you are more likely to catch coding regions
What is serial analysis of gene experssion (SAGE) sequencing? - Answer 1. SAGE library is created from a pool of mRNA
- uses SphI to cut at specific nucleotide bases giving 9-14 bp tags
- cDNA is concatenated and sequenced
- computational tool break up sequences into their tags
- Compare to genome sequence and annotate tags
- gives a count/quality of expression levels of genes
What are some problems associated with Serial analysis of gene expression (SAGE)? - Answer 1. tags may match to multiple genes
- if you are working with an organism that does not have a sequenced genome, tags may not match to any gene.
What is RNA-seq - Answer Transcriptome profiling using deep sequencing techniques. Typically uses illumina sequencing
How are genes represented on Affymatrix Gene Chips? - Answer by 25 mers in 2 versions, 1 perfect match and 1 mismatch. Perfect match - mismatch = intensity value of the probe pair
What are the steps for an Affymatrix Gene Chip experiment? - Answer 1. primer hybridization 2.reverse transcription (first strand cDNA synthesis)
- 2nd strand cDNA synthesis
- clean up of double stranded cDNA synthesis
- amplification and biotin labelling of antisense cDNA
- clean up of biotinylated cDNA
- fragmentation
- Hybridization
- washing/staining
- Scanning
What are the drawbacks of gene chips? - Answer 1. are not available for all genes/genomes
- can be difficult to distinguish between close gene copies (homologs/paralogs)
- expression may be higher than when the spot is saturated
- difficult to deal with dye bias and background noise.
What are the 2 RNAseq analysis methods? - Answer 1. Align reads to genome
- De novo assembly
What are 2 methods used to DETERMINE protein structure? - Answer 1. Xray crystallography
- NMR Spectroscopy - estimates distance between nuclei in a magnetic field
What are 4 methods to PREDICT protein structure? - Answer 1. protein modeling
- homology modeling - use sequence homology to a known protein to predict structure
- threading - build models based on existing 3D structures and compare the unknown to these models
- ab-initio modeling - predict structure without prior knowledge
What are some problems that occur with proteomics techniques? - Answer 1. protein-protein interactions
- post-translational modifications
- requires very clean crystals
What are 3 large scale protein study techniques? - Answer 1. Immobilized- gradient 2D PAGE
- N-terminal sequencing
- Mass spectrometry
What dimensions are proteins typically separated by in immobilized gradent 2D PAGE - Answer 1. isoelectric focus (pH)
- molecular weight
what does PAGE stand for (2D PAGE)? - Answer Polyacrylamide gel electrophoresis
How does N-terminal sequencing work? - Answer Amino acid residues are cleaved one at a time, and are analyzed by high performance liquid chromatography
What are 3 mass spec techniques? - Answer 1. Electrospray ionization mass spectrometry (ESI-MS)
- Matrix assisted laser desorbtion ionization mass spectrometry (MALDI)
- MALDI-TOF (time of flight)
What is phasing in genome assembly? - Answer Assemble DNA into pseudochromosomes and identify alleles in each of the chromosomes
what is HiC? - Answer Chromosome confirmation capture sequencing
What does TargetScan do? - Answer searches 3' UTR for miRNA reverse complement sequences
What are the 3 methods of DNA methylation? - Answer 1. during replication (at the replication fork)
- Due to histone methylation
- siRNA directed de novo methylation
What are some reasons DNA may be methylated - Answer 1. genome maintenance and control of transposon activity
- parental genomic imprinting (plants/animals)
- X-Chromosome inactivation (female mammals)
- Hypermethylation of tumor supressor genes (cancer biology)
- transgene silencing
- regulation of genes during development
What are the steps involved in Bisulphite genomic sequencing? - Answer 1. fragment DNA
- add adaptors 3.treat with bisulphite (converts unmethylated cytosine to uracil)
- PCR amplify
- NGS sequencing
- Analysis
- map to genome
What is commonly used as a control in bisulphite sequencing? - Answer Chloroplast DNA because it is entirely unmethylated
What is ChIP sequencing and what is it used for? - Answer Chromatin ImmunoPrecipitation Sequencing. Used to identify DNA sequences that proteins bind to.
What are the steps involved in ChIP sequencing? - Answer 1. cross-link proteins to DNA
- shear DNA strands by sonicating
- add bead attached antibodies to immunoprecipitate the target protein
- unlink protein and purify DNA
- sequence
- map to genome
What does NCBI stand for? - Answer National Center for Biotechnology Information
What databases are apart of the International Nucleotide Sequence Database Collaboration (INSDC) - Answer GenBank, EMBL, DDBJ
What can sequence data in NCBI be linked to? - Answer proteins/DNA, taxonomy, genome, mapping, protein structures and domains, and PubMed Journal Literature
What are the 3 sections of a GenBank flat file? - Answer 1. Header - information that applies to the entire file
- Features - describes the annotations of the sequence
- Sequence - nucleotide or amino acid sequence
What information is in the header of a genbank flat file? - Answer Locus name, length of
What are missense mutations? - Answer changes the AA produced
What are non-sense mutations? - Answer changes the AA to a stop codon
What are silent mutations? - Answer change in nucleotide sequence that does not change the AA. This usually occurs in the 3rd codon position due to the tRNA wobble
What are frameshift mutations? - Answer Either an insertion or a deletion that affects all of the following AA.
What is sequence identity? - Answer The % of positions where the nucleotide or amino acids are an exact match
what is sequence similarity? - Answer The % of positions where the sequence has a similar match. This is based on groups and biochemical properties. Only applies to amino acid sequences.
What is sequence homology? - Answer A qualitive measure of the relatedness between 2 sequences. This is an absolute value, so sequences are either homologous or not.
What are the 3 choices that can occur for each base pair position when aligning 2 sequences? - Answer 1. The sequences should be aligned with each other
- Seq1 should have a gap
- Seq2 should have a gap
What does BLAST stand for? - Answer Basic Local Alignment Search Tool
What are the 4 types of BLAST? - Answer 1. BLASTN - Nucleotide query to nucleotide database
- BLASTP - protein query to protein database
- BLASTX - Nucleotide query (translated) to protein database
- TBLASTX - Nucleotide query (translated) to nucleotide database (translated)
What are the step of a BLAST search? - Answer 1. index words
- the target database is searched for matching words
- the matching words are extended until the score of the alignment drops off
How are nucleotide sequence alignments scored? - Answer matches are given a + value, and mismatches are given a - value. Point mutations and segmental mutations are taken into account
How are amino acid sequence alignments scored? - Answer Scored based on how some AA substitutions are better than others. Typically based on BLOSUM or PAM matrices.
What does BLOSUM stand for? - Answer BLOcks SUbstitution Matrix
What does PAM stand for? - Answer Percent Accept Mutations
What does the number in a BLOSUM matrix mean (ex. BLOSUM62)? - Answer It is the % identity between species. So a lower number is for more distantly related sequences and a higher value is for more related sequences.
What is a BLAST E-value? - Answer The expect value. It is the likelyhood that the alignment is significant. The number of alignment that are expected to find with a score greater than or equal to the score you have in a search against a random database. The lower the value the better.
What unix command allows you to create a BLAST database? - Answer makeblastdb
What file extensions will be created when making a command line nucleotide BLAST database? - Answer .ndb, .not, .ntf, .nsq, .nhr, .nin
How does ClustalW work? - Answer it uses a guide tree (created by neighbour joining) for multiple sequence alignments. It generates a pairwise distance matrix for all of the sequences. It does pairwise alignments of the outer branches, creating sequence profiles. The sequence profiles are aligned to make a full sequence alignment.
What is MAP for EST contig assembly? - Answer Multiple alignment program. Terminal and long internal gaps are not penelized. The user supplies the scoring parameters. Uses plain sequence data. Works with either nucleic acid or protein data. Runs in Unix.
What is CAP for contig assembly? - Answer Contig assembly program. Uses base quality values for overlaps and consensus sequence. Uses genomic or EST data. Runs under UNIX.
What are the steps of CAP? - Answer 1. remove poor quality end reads
- computation of overlaps between reads
- removal of false overlaps
- construction of contigs
- construction of multiple sequence alignments and generation of a consensus sequence
what is Phrap? - Answer Fragment assembly program. Uses base quality values for overlaps and consensus sequence. works with EST or genomic data. takes trimmed phred files as input
What are the steps of Phrap contig assembly? - Answer 1. read in files
- find pairs of reads with matching words
- Smith waterman comparison (SWAT)
- sort matches and assemble by progressive merging of pairs with high scores
- create mosaic consensus sequence of individual reads
What are the categories in the Nucleic Acids Research database issue? - Answer 1. nucleic acid sequence and structure, transcriptional regulation
- protein sequence and structure, motifs and domains, protein-protein interactions
- metabolic and signalling pathways, metabolites, enzymes, protein modification
- Viruses, bacteria, protozoa, and fungi
- human genomes, model organisms, comparative genomes
- genomic variation, diseases and drugs
- Plant databases
- other molecular biology databases
What is GMOD? - Answer generic model organism database. An opensource project to develop a complete set of software for creating and administering a model organism database.
What tools does GMOD include? - Answer genome visualization and editing tools, literature curation tools, database schema, biological ontology tools, a set of standard operating tools
What are some examples of Databases that are built on GMOD? - Answer WormBase, FlyBase, Mouse Genome Informatics, Gramene, Rat Genome Database, TAIR, EcoCyc, Saccharomyces Genome Database
What do function centric databases focus on? - Answer metabolic pathways, protein function, classifications
What are some examples of a metabolic reconstruction database? - Answer KEGG, WIT2, MetaCyc
What is the difference between a file system and a relational database - Answer File systems store data in files, relational databases store information in tables.
