| what does bioinformatics deals with? | any thing that interests biologists , DNA/protein sequences, DNA variation, Gene expression (microarrays), data from experiment , images/models, articles. |
| what are the first methods of DNA sequencing? | maxam- gilbert it was based on chemical reactions using large amounts of purified , end-labeled DNA, not used at large scales and sanger sequencing using small amounts of DNA in any form its enzymatic. |
| what is Shotgun sequencing? | its a large scale sequencing on random DNA strands (used for the first genomes) , used restriction enzymes to cut large fragments into short ones making genomic libraries which are then separated and sequenced , then finally assembled on overlapping regions. its expensive and laborious . |
| what's high-throughput sequencing ? | this is intended to lower the cost of DNA sequencing , with the standard dye-terminator method increasing the speed. it applies to exon, genome sequencing transcriptome profiling. |
| what are the main NGS platforms? | illumina solexa (1-6 GB),ABI solid (80-100Gb), paBio ( 100-200gb) |
| what happed to the cost of DNA sequencing in the NGS era? | the cost of Sequencing stimulated by the genome project decreased drastically in an exponentially, and it also became much faster. |
| why did the cost of sequencing decrease? | because of the increase of pre-processing (sample collection) and post processing (bioinformatic analysis). that's why its important in all labs. |
| how is the genome analyzed? | storage of primary sequences, assembly of chromosomal sequences, predictions of gene locations, gene annotation (predicting their function),chromosome composition (variation). |
| what's metagenomics? | it involves directly sequencing samples from various locations, samples of living organisms in their natural environments. to identify the species, characterize their abundance, discover new protein. |
| what is the DNA chip technology ? | 1-cell culture/tissue,2- RNA extraction, synthesis of florescent cDNA |
| what's transcriptome analysis? | its defined as the set of all RNA molecules transcribed from genome ,gene expression is tightly regulated each expressed at a different level depending of cell type, tissue, time. |
| what are the two types of proteome analysis ? how to they work? | (2D-page) electrophoresis , and chip on chip analysis : by first tagging of transcription factors with a protein fragment they immobilizing it with fixative agents, fragmenting dNA then Precipitation of DNA-protein complexes, then unbinding them. measurement of DNA enrichment when two extracts are co-hybridized on microarray(chip) each containing one DNA fragment likely to bind. |
| what's an intractome? | a network of complexes. |
| why do we need biological data bases? | 1- for storing and communicating large datasets, 2-make these datasets available for scientist,3- making data available in computer-readable forms. |
| what are some examples of bimolecular databases? | sequence and structure databases (UniPort), genome sequences and annotations (NCBI), molecular functions (EXpasy), biological processes (GeneNet) |
| what's the difference between primary and secondary (derived) databases? | primary databases are experimental results directly inputed into databases , secondary databases are results of analysis of primary databases, aggregate of many databases have links to other data items, combination of data and consolidation data. |
| what's the availability of databases? | its publicly available no restriction, with copyright , not downloadable, academic but not freely available , commercial . every year new databases are created with the first issue being open access. |
| what are some nucleic sequence databases ? | GenBank 1979 USA, EMBL-EBI 1974 UK,and DDBJ 1986 Japan |
| what's the INSDC? | ints the international nucleotide sequence database collaboration of (DDBJ, EMBL-EBI, and NCBI) |
| what is the rule with regarding publishing articles that have sequencing? | the sequence has to be deposited in a reference database in any of the 3 databases, they are automatically sincronised. |
| what's the sequencing pace ? | nucleic sequences , Entire genomes, protein sequencing (by translation of gene not direct) |
| how is data of sequences submitted? | direct submission from author by web or email, sequences between banks is identical. |
| what are the sequence format? | Fast A, GenBank (protein ID N) |
