Chapter 2: Networking - Homework

David Steffen, Ph.D.
President, Biomedical Computing, Inc.
6626 Westchester
Houston, Texas 77005
USA

For each homework problem, describe how you solved the problem (where appropriate) and show the results you obtained.

Problem 1:

Read the following message which appeared on a bionet newsgroup and answer the questions which appear after it:
(I have edited this message for the purposes of this homework. Considerably more information is given in the original message.

From: etzold@embl-heidelberg.de
Newsgroups: bionet.software
Subject: access to SRS-WWW databank browser
Date: 15 Jul 94 23:48:58 +0100
Organization: European Molecular Biology Laboratory

I must apologize to all who had problems accessing the SRSWWW server.
[...] the address www.embl-heidelberg.de has been
moved to another machine and it seems there are some nameservers that
have still the old address

regards
Thure Etzold
  1. Is the SRSWWW server now on the old computer or the new computer?
  2. Do the old computer and the new computer have the same or different IP addresses?
  3. Do the old computer and the new computer have the same or different names?
  4. The difficulty is caused by "some nameservers". What ought these nameservers to be doing, and what are they doing instead?
  5. If your nameserver is one of these problem nameservers, and if it is run by a cretin who refuses to fix it, what could you do to use the SRSWWW server? (This requires some additional information from Thure. Assume you can and have obtained this in your answer.)

Problem 2:

Supposing all you know about BioMOO is that the machine it is on is named: 
bioinformatics.weizmann.ac.il
  1. Use telnet to contact this machine. What happens?
  2. What piece of information are you missing, and how would it help to contact BioMOO?
  3. (Extra Credit) Think of as many ways as you can to obtain this extra piece of information.

Problem 3:

There are many ways to skin a cat. It is important to know these different ways, because if one fails you need to be able to try another. In the Multiple Sequence Alignment chapter, you will need to obtain a number of immunoglobulin sequences for alignment. These sequences are present in the PDB database. However, you will already run into trouble with the first of these, as the PDB accession number listed for it is obsolete. In this problem, you will be required to try several approaches for obtaining a sequence.
  1. Connect to SRSWWW, go to PDBFINDER, and search for the PDB Accession Number 3FAB. (You should retrieve nothing).
  2. Pretend that one of your fellow students tells you that the sequences you need to obtain from PDB 3FAB are in fact the sequences B49444 and A49444 from PIR. Use the Genbank Retrieve email server to obtain these two sequences.
  3. One approach to obtaining a sequence from the literature if all or part of the sequence is printed in the journal is to type in a bit of the sequence you want and search for it with one of the sequence similarity tools. Use BCM search launcher to search the protein databanks for the following two sequence fragments:

                SCQVTHEGSTVEKTVAP

            NVNHKPSNTKVDKKVEP

  4. Suppose all you know about the sequence you want is that F.A. Saul and R.J. Poljak are the authors on the paper reporting the sequence. Use Entrez to find the most probable sequences.
  5. Finally, let us suppose that in fact all you know is the obsolete PDB accession number 3FAB. Obviously, searching SRSWWW has failed. What is left to try? Try that.

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David Steffen
steffen@blkbox.com