EL's+Milestone+-++Analysis+the+sequence+alignment+of+NPC+protein

Analysis the sequence alignment of NPC protein

There is a sequence of EF619930 ORIGIN 1 gaatagcggc gcgattcgcc cttagagttt gatcctggct cagattgaac gctggcggca 61 tgccttacac atgcaagtcg aacggcagca cgggtgcttg cacctggtgg cgagtggcga 121 acgggtgagt agtgcatcgg aacgtaccca gtagtggggg ataactaccc gaaagggtgg 181 ctaataccgc atatactgtg cgcaggaaag caggggaccg taaggccttg tgctactgga 241 gcggccgatg tcagattagc tagttggtgg ggtaaaggcc taccaaggcg acgacctgta 301 gcgggtctga gaggatgatc cgccacactg ggactgagac acggcccaga ctcctacggg 361 aggcagcagt ggggaatttt ggacaatggg ggcaaccctg atccagccat gccgcgtgag 421 tgaagaaggc cttcgggttg taaagctctt tcggacggaa agaaaacgga tgggttaata 481 ccctgttcgg atgacggtac cgtcataaga agcaccggct aactacgtgc cagcagccgc 541 ggtaatacgt agggtgcgag cgttaatcgg aattactggg cgtaaagcgt gcgcaggcgg 601 ttgattaaga caggcgtgaa atccccgggc ttaacctggg aactgcgctt gtgactggtc 661 ggctagagta cggcagaggg gggtggaatt ccacgtgtag cagtgaaatg cgtatagatg 721 tggaggaaca ccgatggcga atgcagcccc ctgggccgat actgacgctc atgcacgaaa 781 gcgtgggtag caaacaggat tagataccct ggtagtccac gccctaaacg atgtcaacta 841 gttgttggga gggtaaaacc ttttagtaac gtagctaacg cgtgaagttg accgcctggg 901 gagtacggcc gcaagctaaa actcatagga attgacggga cccgcacaag cggtggatga 961 tgtgattaat tcgatgcaac gcgaaaacct tacctactct tgacatgtca gagatccctg 1021 agagattggg gtgctgctgc aagaaatctg aacacagtgc tgcatgactg tcgtcagcct 1081 cgtgtccgtg agatgtagga taagatccgc aagcggtcct aaccattgtc gtaagtggcc 1141 atcaataggg ttggggccac ttttaacc
 * l **Use the NCBI database to perfore sequence alignments** ||
 * Explore NCBI websitehttp://www.ncbi.nlm.nih.gov/Search -> CoreNucleotide -> put EF619930 (this is an example)

Take 3 characters to match the amino acid protein sequence. Find the synthesis point by using anaylsis program, Oligo 4 and MacVector. -> There are mostly 3 possibilities that sequence can be. || (A final aspect of sequence alignment that should be considered is evaluation of the accuracy of the alignment. The best way to assess the accuracy is to compare alignments from sequence comparisons with alignments from protein three-dimensional structures. Of course this assessment is possible only if you are working with a family of proteins for which three-dimensional structures are known for at least two members of the family. The alignment obtained by including tertiary structural features provides a set of test alignments against which sequence-only alignments can be compared. Similar conditions can then be applied to sequences from the family for which three-dimensional structures are not available.)
 * Identity:** considers only identical residues
 * Genetic Code:** considers the number of base changes in DNA or RNA to interconvert the codons for the amino acids
 * Chemical Similarity:** considers the physico-chemical properties (e.g., polarity, size, charge) with greater weight given to alignment of similar properties
 * Observed Substitutions:** considers substitution frequencies observed in alignments of sequences.
 * Observed Substitutions:** considers substitution frequencies observed in alignments of sequences.