Open the contig (double click on the icon). Choose both sequences from the main project window, and click "assemble automatically" (the button is on top of the project window). Now we want to put them together in a contig. Why did we throw out the bases at the end of the sequences?.Why did we throw out the bases in the beginning of the sequences?.Do the same for the reverse sequence.Īnswer the following questions (base your answers on the chromatograms): Cut off the first 20 bases, and shorten the sequence at the end to 600. Open up the Forward sequence (double click on it) and then click the "Show Chromatogram" button on top of the window. The first thing we have to do is clean them up at the ends. You now have a project with two sequences in it. Make sure you have both the forward (F) and reverse (R) files! ab1 files from both sequence folders (one at a time). From the file menu, choose "Import - Sequences" and choose the. Now we are going to look at the chromatograms.ĭownload a demo copy of Sequencher (unless you are in the classroom, or your lab has a licensed copy, in which case you can use the "real" thing).Ĭlick on the link and follow the directions for downloading. Look at the Taxonomy - what organisms do we have hits in?.Look at the blast result - which gene is this?.How many open reading frames were found? Given that this is the middle of a protein, which do you think is the correct one?.From what base to what base of the original sequence is the cleaned sequence?.Open the folder, go into the folder called "2682_Bro-mII-R" and double click on the index.html file.
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Double clicking may be enough, and you may have to use a program, such as WinZip (if your computer doesn't have it, it can be downloaded free at: ) Unzip the file, and then you'll have the folder "DNAseq".
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If you are working on a PC, it should download a zipped file whose name starts with "DNAseq". Usually a double click will upzip it, but you may have to use the program StuffIt Expander (found in the Applications folder, and then in the Utilities folder). If you are working on a Mac, it should download and open a folder on your desktop called "DNAseq" - some computers will not open it automatically, it will just download.
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Log in with the userid bipstd02 - the password is the same as the userid.Ĭlick on the DNAseq tab on top, choose both sequences, and click download You receive an email that your sequence is waiting - now you have to download. You set up a PCR and send it to the sequencing unit with primers in both directions to be sure your sequence is correct.
Read through the assignment carefully before you start!! It will make answering the questions easier!!Ĭongratulations! You've started a new project in the lab, and the first thing you have to do is clone your gene of interest. Assignment #2 Assignment 2: Sequence Download and Assembly
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