Bioinformatics (8) 썸네일형 리스트형 Phylogenomics phylogenetic tree : diagram showing inferred evolutionary relationship chloroplast&mitochondria genome sequences are usually used to draw phylogenetic tree It is because that they contain their own genome sequences and they are based on maternal inheritance Moreover, their sequences are more short and simple than nuclear genome 1. NCBI에서 유전체를 genbank format으로 다운로드 받는다 2. 다운로드 받은 유전체에서 유전자들이 만들어내.. Python4 - group of funtions, but is not built in default python - have to import to use - Biopython sys.argv[#] - refers the designated files using number and carries out coding contents Usage import sys openfile = open(sys.argv[1], 'r').readlines() openfile = open(sys.argv[2], 'r').readlines() Command python2_python_file_name_file_name[1]_file_name[2] os.system() - executes linux funtion by python glob.. Python3 .split() - separates a string into multiple strings, arranges them in a list, and returns the list according a defined separator note! default separator is any whitespace Example string = 'Gm01:1234..5678:Gm01g12345' string.split(':')[1].split('..')[0] = '1234' .strip() - removes all the leading and trailing spaces from a string .replace('a' , 'b') - replaces all the 'a' into 'b' in a string .ap.. Python2 indexing - returns the index position of an element or an item in a string of characters or a list of items slicing - returns a slice object in a string or a list Python1 dictionary dic_a = {'English':'영어'} → dic_a ['English'] = '영어' Usage →dict_amino_acid = {'AUG':'Met', 'UGU':'Cys'} →dict_amino_acid = {} dict_amino_acid['AUG'] = 'Met' →key = ['AUG', 'UGU'] value = ['Met', 'Cys'] dict_amino_acid = dict(zip(key,value)) python coding vi_file_name.py python2_file_name.py input() - prompts the user for data that in converted to and returned as a integer raw_input() .. Linux - Ubuntu Command ls : shows files which are located at present directory and lower directory ll : plays very similar as ls, but it shows file information in more detail vi editor : shows file contents, you can edit or make new file contents using this command →vi_file_name →insert : edit mode →Esc : quit edit mode + wq(!) mkdir : makes a new directory →mkdir_directory_name cd : changes directory - relati.. Sequence Alignment Global alignment : a type of pairwise sequence alignment where two sequences are generally similar over the length as it is the end-to-end alignment of two strings and takes account of entire sequences Local alignment : a type of pairwise alignment where two seqeunces are not assumed to be similar over the entire length, and it finds the regions with the highest level of similarity between the t.. Genomics basic concept DNA(Deoxyribonucleic acid) : a helical molecule comprising a sequence of four nucleotides(bases) RNA(Ribonucleic acid) : a single-stranded molecule comprising a sequence of four nucleotides Protein : a molecule comprising a long chain of amino acids connected by peptide bonds Gene : a strctch of DNA containing the information necessary for coding a protein/polypeptide Central dogma Duplication T.. 이전 1 다음
