• some programs do not have GUI
• keeping track of your work
• almost all scientific servers run Linux/Unix

• on linux or mac:stfp or scp
• on windows putt: pscp or transfer window

• conservation of the order of functional elements in regions of the genome between species 
• assign function and elucidate evolution

• transcription factors 
• rna polymerase
• histone modifications

• protein that package and order DNA into structural units 
• histones are subject to a wide variaty of post-translational mods
• these are: enhancer regions promotors transctription and start sites

• functional effects: coding changes,splice sites, regulatory changes
• non-function effects : synonymous, introns, intergenic
• SNPs, Indels, CNVs/SVs

• similarity in sequence due to shared ancestry

• gene that descended from the same ancestral gene seperated by a speciation even

• residue charge
• size 
• hydrophobicity
• rigidity in the an
• a.a. chain
• capacity to form ion and disulfide bonds
• specific roles in active sites

• BLOcks SUbsitution Matrix
• ungapped local alignments of protein families
• group sequances with more than L% indentical amino acids
• derive the sunsituiton matrix with the observed substituion of frequency of amino acids between different groups

• PAM 
• is a subsitution of an amino acid tolerated by natural selection as the protein function does not change

• finds the best alignment across the whole sequences
• used for highly similar sequences of almost the same length

• finds regions of high similarity in parts of the sequences 
• finding sub-sequences within sequences that may have a relation
• best for sequences that share some degree of similarity 

• compensate for insertions and deletions between the sequences

• serves to keep gaps at reasonable number 
• a cost for openning a gap
• cost for the extension or size of the gap

• use dynamic programming to find the alignment with highest score
• simth-waterman(local)
• needleman-Wunsch(global)

• split a problem into small problems, solve each subproblem one at a time, combine the solutions to the subproblem to an overall solution
• advantage is that is very effcient to solve just a series of small problems
• someitmes local solutions may not lead to global optimals

• finds the globally optimal alignment for 2 sequences given a scoring function
• best means highest score for aligning both whole sequences

• basic local alignment search tool
• calculates similarity for biological sequences
• produces local alignment 
• uses statistical theory to detemine if match is by chance

• protein-protein 
• compares an amino acid sequence against a protein sequence database

• nucl-nucl
• compares a nucleotide query sequence against a nucleotide sequence database(for speed not sensitivity)

• translated nucl-protein
• compares the six-frame conceptual translation products of a nucleotide query against a protein sequence database

• protein translated nucl
• compares a protein query sequence against a sequence database dynamically translated in all six reading frames

• translated nucl-translated-nucl
• compares six frame translation of a nucleotide query sequence against the six frame translations of a nucleotide sequance db

• promotor region in higher eukaryites located 28-34 bp upstream of the TSS and is associated with strong tissue specific promoters

iteratively search a query protein sequence,

multiple-sequence alighnment or profile HMM against the target protein sequence DB

• database of protein domain families
• high quality manually curated multiple sequence alignments and profile HMMs