GENETIC TEACHER

Polygenic Inheritance is the process of several genes that interact to produce certain trait which are also responsible for most important traits, Pleiotropic Inheritance is the effect of single gene on more than one trait (Watch Related Video in #geneticteacher) #geneticteacher

Every treatment occurs in each block refer to complete block design, Not every treatment occurs in each block refer to incomplete block design, Mendelian traits refer to discrete variation, Quantitative traits refer to continuous variation, values of Mendelian trait (P/q), Values of quantitative traits (Mean/Standard Deviation) (Watch Related Video in #geneticteacher) #geneticteacher

No interaction between genotypes= Response parallel, Interaction between genotypes= Response different, No interaction between genotypes and environment, Convergence interaction between genotypes and environment, Divergence interaction between genotype and environment, Cross over interaction between genotypes and environment (Watch Related Video in #geneticteacher) #geneticteacher

Gene structure contains (Intergenic region + Promoter binding site or motif + 5 end untranslated region + Transcription start site + Exons + Introns + 3 end untranslated region + Poly-AAA Tail) all of these are important for modeling binding site and gene structure prediction (Watch Related Video in #geneticteacher) #geneticteacher

Bioinformatics is the study of inherent structure of biological information for understanding data of structural biology and biochemistry and molecular biology and genomics and computer science and statistics and mathematics, Motifs and gene structure are important elements during work in bioinformatics for modeling binding site and gene structure prediction, Pairwise score matrix is important for phylogenetic tree construction (Watch Related Video in #geneticteacher) #geneticteacher

For BLAST Sequences the input query must be Amino Acid Sequence or DNA Sequence, For Amino Acid Sequence (BLAST P compares against protein sequence database) (T BLAST N compares against translated nucleotide sequence database), For DNA sequence (BLAST N compares against nucleotide sequence database) (BLAST X compares against protein sequence database) (T BLAST X compares against translated nucleotide sequence database) (Watch Related Video in #geneticteacher) #geneticteacher

Conserved Multiple Sequence Alignment Regions help to identify functionality. Percent sequence identity describe invariant of two nucleotide or amino acid sequences (Match sequence) (Mismatch sequence) (Gap Opening) (Gap Extension) (Watch Related Video in #geneticteacher) #geneticteacher

Goals of Local Alignments: 1- To compare short sequence to large one, 2- To compare a single sequence to entire database, 3- To compare partial sequence to the whole sequence, 4- To identify newly determined sequences, 5- To compare new genes to known ones, 6- To guess functions for entire genomes full of ORFs of unknown function for similarities between regions of two sequences, Single letters base codes of nucleotides (Watch Related Video in #geneticteacher) #geneticteacher

Pairwise alignment (Arrows refer to identity bar and some what similar for one dot and very similar for two dots and the different between internal., and terminal gap) (Watch Related Video in #geneticteacher) #geneticteacher

For Multiple Sequence Alignment Gather Data for Alignment and Rearrangement the required sequence for alignment (Watch Related Video in #geneticteacher) #geneticteacher

For BLAST Sequence by NCBI.: 1- Choose the required sequence as query, 2- Select BLAST program, 3- Choose the database to search, 4- Adjust the optional parameters and click BLAST. The output of BLAST are (Graphic Display + Hit List + Alignment). In Graphic display (Red Color refer to excellent BLAST, Pink Color refer to pretty good BLAST, Green Color refer to OK BLAST, Blue Color refer to Bad BLAST, Black Color refer to really bad BLAST, Longer matched sequence segments refer to better BLAST. In addition BLAST Hit List provides accession number that links to gene bank and genome link and expected value as indicator of how good match to query sequence and score that refer to link alignment (Watch Related Video in #geneticteacher) #geneticteacher

For search any gene across NCBI type gene bank in google search and select gene bank Home-NCBI and type the required gene in nucleotide search and select the results in FASTA format and enjoy the sequence of gene (Watch Related Video in #geneticteacher) #geneticteacher

Input sequence of the online primer 3 tool must be in FASTA format (Watch Related Video in #geneticteacher) #geneticteacher

For PCR primer design in NCBI go to primer design tool in NCBI and type or paste required sequence in FASTA format and adjust primer parameters and click on get primers (Watch Related Video in #geneticteacher) #geneticteacher

For sequence assembly gather sequence in queries and use Contig assembly software to get assembly sequence, If the required nucleotides for assembly 177 nucleotides (only 35 nucleotides assembled) (Average coverage for assembly=7X) (Watch Related Video in #geneticteacher) #geneticteacher

To search open Reading Frames in NCBI site go to ORF finder then type or paste required DNA sequence and press ORF find after that click on six frames because any gene has six frames and enjoy the results of ORF (Watch Related Video in #geneticteacher) #geneticteacher

Phylogeny is the study of the evolutionary relationships between biological entities, Orthologous genes found in a single copy in the genome and presented homologues between species, Paralogous genes results from duplicated genes and found in more than one copy in the genome (Watch Related Video in #geneticteacher) #geneticteacher

The studies of horizontal gene transfer different between species tree and gene tree, in species tree the gene transfer from species B to species C and D, in gene tree the gene transfer to sequence C and B while Sequence A and D called speciation (Watch Related Video in #geneticteacher) #geneticteacher

Cladogram refer to no genetic meaning between taxonomies. Phylogram refer to genetic change between taxonomies. Ultrametric tree define time changes between taxonomies (Watch Related Video in #geneticteacher) #geneticteacher

Node is a branch point in tree. Branch define the relationship between taxonomy of ancestries. Branch Length represent the number of changes that occur in branch. Root is the common ancestries of all taxonomies. Clade is a group of two or more taxonomies that includes common ancestors. Monophyletic Group or clade refer to (Group-1). Paraphyletic Group refer to (Group-2). Polyphyletic Group refer to (Group-3) (Watch Related Video in #geneticteacher) #geneticteacher

Southern Blot use to detect DNA. Northern Blot use to detect RNA. Western Blot use to detect protein. In Southern blot technique DNA must be extracted and digested by restriction enzymes then detect digested bands by agarose gel electrophoresis after that blot agarose gel by blotting buffer to easy use probe and detect blotting gel with probe by X-ray film (Watch Related Video in #geneticteacher) #geneticteacher

The Genome Analysis Pipeline can be created from sequencing and assembly of in vitro DNA or cDNA and all of these can be used for gene prediction for annotation to get gene regulation studies and the sequences weighting algorithms attempt to compensate sequences (High weights sequences located in one group) (Low weights sequences located in another group)in a Phylogenetic Tree (Watch Related Video in #geneticteacher) #geneticteacher

Sequence Motifs are a short recurring patterns in DNA that are presumed to have biological function. So to identify motifs the genes are turned ON/OFF by regulatory proteins and these proteins bind to upstream regulatory regions of genes to either attract or block RNA polymerase then regulatory proteins or Transcription Factors binds to short DNA sequence called motifs or Transcription factors binding sites so finding the same motif in multiple genes regulatory regions suggest regulatory relationship among those genes. Motifs profiles and consensus create by line up the alignment sequence patterns by their start indexes to construct matrix profile with frequencies of each nucleotide in columns to consensus nucleotide in each position that has the highest score in each column (Watch Related Video in #geneticteacher) #geneticteacher

Every gene in organisms contains regulatory regions stretching from 100 to 1000 base pairs called upstream of transcriptional start site which located within regulatory regions which called transcription factors banding sites or motif therefore transcription factors or motifs influence gene expression by binding to specific location in the respective gene regulatory regions. Hence transcription factor binding sites can be located anywhere within regulatory region and may vary slightly across different regulatory regions because non essential bases could mutate because RNA polymerases used for initiation complex of transcription binding sites: (RNA Poly-1 specific for Ribosomal RNA) (RNA Poly-2 specific for all protein genes) (RNA poly Poly-3 specific for Transfer and Ribosomal RNA) (Watch Related Video in #geneticteacher) #geneticteacher

Eukaryotic mRNA Gene consist of (Enhancers, Promoter, TATA Box, Exons and Introns). Promoter and TATA Box have 300 base pairs while TATA Box have only 30 base pairs from the 300 base pairs. Typical Promoter consist of three regions (-35 Region (TTGACA), -10 Region (TATAAT), RNA Start Region (A/G)) (Watch Related Video in #geneticteacher) #geneticteacher

SSR or Simple Sequence Repeats Markers are a DNA markers developed by amplifying repeated microsatellite across genome. SSR markers called Dominant markers. Polymorphism of Co-dominant markers have heterozygote and homozygote bands and polymorphism of Dominant markers have only homozygote band. The band that has low molecular weight refer to low amplified nucleotides while the band that has high molecular weight refer to high count of amplified nucleotides (Watch Related Video in #geneticteacher) #geneticteacher

The process of plant breeding by markers are creating by searching of genetic variability and genetic distance and pedigree validation by using marker assisted selection to evaluate hybrid purity and make fingerprint for right enforcement in multiplication and commercialization. For example if we have two parents the first generation called F1 and for marker assisted selection must create backcross hybrids for many generations to get whole genome selection. For fine marker assisted selection results studied properties must be polymorphic and reproducible and easy fast and selectivity neutral and co-dominant inheritance through genome to get high resolution results (Watch Related Video in #geneticteacher) #geneticteacher

Haplotype are a multiple loci in the same chromosome that are inherited together, usually linked in a string of SNPs results, to form haplotype block must create recombination in each chromosome by meiosis mating fashion for generations, therefore haplotype are a collection of alleles derived from same chromosome (Chromosome phase in genotypes Unknown) / (Chromosome phase in haplotypes Known)(Watch Related Video in #geneticteacher) #geneticteacher

Linked genes (Near between each other), Not linked genes (Have big distance between each other), Shapes of homozygote and heterozygote nucleotides in sequence results (Watch Related Video in #geneticteacher) #geneticteacher