Good morning! You have attempted to submit jobs in batches
last night and the computer worked very hard for you at night.
Presumably, the results are ready for analysis by now. Please
analyze your results in the following aspects:
Connect to GeneMark
(GeneMark at EBI) and
submit your seq for analysis. (use your own E-mail
address to receive the graphic representation.)
Use your seq. as a query to submit a blastn job (use
nucleic acid to search nucleic acid database) to GCG
FTP your blast results back to PC and store them
under tblastn subdir
Go to subdir , open genome_ide.xls => Select the
main item "ORF File Util", then select
"Import ORFx blast"
Now you will be able to view your blast results from
this Excel table. Alternatively, you can use VisualBlast
(we will not teach how to use this software until the
3rd day) to examine the tblastn files one by one.
Please make a preliminary assignment based on your
blast results, and fill it in the column labeled as
"Similar to ... (tblastn)". If there is no
matche, label it as "none".
Create a subdirectory call "tblastn" in FTP to . Transfer all your tblastn
file to this new subdir.
Transfer your POST
file to FTP to
Please submit your seq. for tRNA
scan (a local example of tRNA
Please compare the rRNA sequences (query) against
your seq (databank) using FastA.
Examples used in the class
- Results of ORF analysis of the
- Results of tRNA scan