Main Page | Directory
Summary of tools for DNA and Protein Analysis
| 1. GCG |
is a subset of programs that run on top of UNIX. It can be accessed (via UNIX) at the
UNIX prompt |
- has a manual and a list of commands which can be accessed through genhelp or genmanual
- motifs of a peptide sequence will help find dominant features that are common in
protiens
- pileup 2 lines or more of sequences (protein or DNA) to see similarities and
differences between sequences
- blast is a program that retrieves similar sequences (to a query sequence from a
specified database (e.g.: PIR which is a protein database
- fetch will obtain more information about other similar sequences obtained in the
blast search
| 2. UNIX Commands |
These commands can be executed at the UNIX prompt |
- ls lists files in your UNIX accout
- ls -la | more is a more detailed listing of files, sizes, hidden files, and
permission access
- mkdir [directoryname] will create a directory to store files
- rm [filename] will remove a file
- ftp [hostname] moves files from one account to another
- cp [oldfilename newfilename] will copy a file to a new file
- mv [filename ~/directoryname] will move files from one directory to
another
- cd [directoryname] changes a directory and helps to move around the file
hiearchy
- history gives a list of previous commands entered; this is useful when you forget
the name of the file that you just accessed
- vi [filename]is an editor that is provided on the sac server; it has two
modes. the edit mode [ESC] and the insert mode [capital i]. To exit and save your work
press [shift ZZ]
| 3. Internet Searches |
These are some really good search engines |
- Metacrawler
| :is a search engine useful in finding information. It utilizes a number of
different search engines to find information and compiles a list of sites that match your
query |
|
- Electric Monk
| : allows you to ask a question rather than a one work query; it is more of a
novelity rather than a true search engine |
|
- Yahoo
| :another search engine which allows you to send a query and gives related sites
(urls) back; it's not as good as Metacrawler (or at least I think so) |
Webmaster: Alan Kapadia.
Questions, Comments,
Concerns...E-mail me: akapadia@nbcs.rutger.edu.