Assignment -
Choose genes that are trnF- trnL genes.
Curcuma longa (plant)
Choose Curcuma, globba and zingiberales to blast them. Should limit the organisms (taxa ID).
Collect the sequences with correct E- values
Use just NBCI web
Collect minimum 20 sequences for each plant.
Collect the sequences and copy, past them on the word program.
The purpose of this problem is to obtain information from the NCBI website. The RefSeq accession number of human beta globin protein is NP_000509. Go to NCBI. What is the RefSeq accession number of beta globin protein from the chimpanzee (Pan troglodytes)?
(1) There are several different ways to solve this. Try typing chimpanzee globin into the home page of NCBI; or use the Taxonomy Browser to find chimpanzee Entrez Gene entries.
(2) HomoloGene is a great resource to learn about sets of related eukaryotic proteins. Use HomoloGene to find a set of beta globins including chimpanzee. The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp, then matched up and put into groups, using a taxonomic tree built from sequence similarity, where closer related organisms are matched up first, and then further organisms are added to the tree. This means that Homologene gives you information about the similarity between protein sequences for all of the species presented (mammals, plants, fungi etc.).
Accessing information from UCSC. Hemoglobin is a tetramer composed primarily of two alpha globin subunits and two beta globin subunits. Consider alpha globin. There are two related human genes (official gene symbols HMI and HBA2). Use the UCSC Genome Browser to determine the length of the intergenic region between the HBAI and HBA2 genes.
Question: The purpose of this problem is to introduce you to using Entrez and related NCBI resources. How many human proteins are bigger than 300,000 daltons? What is the longest htsaagrotein? There are several different ways to solve these questions.
(1) Try to first limit your search to human by using TaxBrowser. From the home page of NCBI select the alphabetical list of resources and find the Taxonomy Browser and the entry for human. Then follow the link to Entrez Protein, where all the results will be limited to human.
(2) Enter a command in the format xxxxxx:yyyyyy[molwt] to restrict the output to a certain number of Daltons; for example, 002000:010000[molwt] will select proteins of molecular weight 2,000 to 10,000.
(3) As a different approach, search 30000:50000[Sequence Length]
(4) You can read more about titin (NP_596869.4), the longest human protein. While the average protein has a length of several hundred amino acids, incredibly titin is 34,423 amino acids in length.
(5) Explore additional ways to limit Entrez searches by using an NCBI Handbook chaptet
(6) redo this exercise for your favourite taxon and then tell me what the largest protein is for this species.
Attachment:- Assignment Files.rar