BCM Search Launcher - Frequently Asked Questions

Questions answered:

• Why have regions of my sequence queries been replaced with runs of X's or N's?
• My sequence is shorter that 7kb, why can't I do a search?
• The server returned an error, what should I do?
  • 500 server error
  • sequence too long error
• Search Launcher Batch Client (SLBC) Questions.
  • The Mac SLBC returns a "Document Not Dated" message, what is wrong?
  • The Mac SLBC does not accept my sequences, what is wrong?
  • The Mac SLBC returned a Bad Address error, what should I do?
  • Can the SLBC be used behind a firewall?
  • What BLAST program and settings should be used to get the best results with BEAUTY Post Processing?

Why have regions of my sequences queries been replaced with runs of X's or N's?

For several of the sequence database search programs used here (including BLAST, BEAUTY, and FASTPAT), each query sequence is filtered for "low-entropy/low-complexity" regions prior to searching. The search options or parameters used for each program can viewed using the [P] link on the search page. This page lists the type of filter that is used for each search.

For protein sequence searches, filtering is performed using the XNU and SEG filters. These filters convert low-complexity regions (such as runs of Q's) to X's -- see the description of the '-filter' option in the BLAST Help Pages. Low-complexity filtering is also described in Altschul et al., (1994) Nature Genetics 6:119-129.

For DNA query sequences, filtering is performed using the RepeatMasker program. The types of repeats are reported, and the repeats and low-complexity regions are converted to N's.

Low-complexity filtering is also described in Altschul et al., (1994) Nature Genetics 6:119-129.

To turn the filtering option off, submit your search using the full-options search form (the [O] link on the search page).

We highly recommend using the filtering option when performing sequence searches. If a sequence does contain a low-entropy region and filtering is not used, then one's search results can be overwhelmed by large numbers of supurious matches to low-complexity regions.

Either the browser that you use or the format of your sequence file may be at fault. Internet Explorer browsers have a much lower effective size limit than Netscape browsers. Some users have found that sequences over 2kb do not work with Internet Explorer.

Since the 7kb sequence size limit is really measured in bytes rather than basepairs, characters like spaces and carriage returns count toward the size limit. For this reason, it is best to use a compact sequence format.

This generally indicates a difficulty with the Search Launcher and we appreciate any information you are able to provide to help resolve the difficulty. To help resolve the difficulty the following information is vital: the time and your host.

Please be as precise as possible with the time. The minute or even second is ideal and be sure to specify the timezone. Your host is the hostname or IP address of the system you are using.

Additional information that can be helpful is: the search performed, any (none) default parameters used, and any data submitted.

We would like to thank you for taking the time to report a difficulty.

This has been a frequent problem with the Internet Explorer browser. If you are using this browser, we recommend that you try the Netscape Navigator.

The limit for many searches is 7000 bytes. Sequences which include numbers and spaces (like a sequence pasted from GCG) approach the 7000 byte limit when the sequence is much smaller than 7kb (the posted size limit). Remove the extra spaces, carriage returns and numbers from the sequence before you submit the search to avoid this error with sequences of 5-7kb.

Our recent upgrade to the Apache 1.3 server software caused a problem with the Batch Client for the Macintosh. Please download the mac-search-launcher-2.6.pl Perl script. The Mac perl script version does not download properly using Netscape to click on the ftp site link. Instead, ftp using Fetch or another (more generic) ftp program to star.bcm.tmc.edu in the pub/software/search-launcher directory with the username anonymous and the password your email address.

You are experiencing this difficulty if you keep getting the help message even when you drop sequences on the MSLBC. First, make sure you are running AppleScript. AppleScript is part of System 7.5 but an extra for older systems. The MSLBC is a MacPerl script and MacPerl 4.1.8 requires AppleScript.

If you are running AppleScript and still having this difficulty, your next best option is to install MacPerl and create a droplet. MacPerl is available here. Once you have installed MacPerl, grab a copy of the Search Launcher Batch Client script here. Start up MacPerl, open the script, then save it as a droplet under a name like SearchLauncher. Drop your sequences on this newly created droplet and you should be asked for the sequence type. If you still get the help message please report the difficulty by sending email.

If you were having difficulty with the original MSLBC but the droplet worked, you will need to leave MacPerl installed on your Mac. If you do not intend to use MacPerl, you might try creating your own runtime instead of droplet by choosing 'runtime' instead of 'droplet' when you save the script from MacPerl. If this works then there is no need to keep MacPerl installed. Please email us if a runtime you create works, it has not worked yet and we would be interested in hearing from you.

There is a limit to the size of acceptable file names on the Mac and PowerPC, use a shorter sequence name so that the "sequence-name.search-tool-name.database-name.html" name is not over about 30 characters. Limiting your sequence name to 10 characters will allow most searches.

Yes, the Search Launcher Batch Client (SLBC) can be used behind a firewall or with a proxy. At this time, for both the Mac and unix systems the hostname and port of the firewall/proxy must be set in the SLBC perl script by editing the script itself. Verion 2.0 or greater of the SLBC perl script is required, it can be obtained here.

To make this script work, be sure you have the hostname and port values of the firewall/proxy. If you are unsure of the port value use the default of 80. In the script look for the word 'proxy' (around line 75). Put your hostname between the two single quote characters towards the end of this proxy_host line, similarly for the proxy_port line. What you need to change looks like ...

$proxy_host = '';
$proxy_port = '';

$proxy_host = 'myhost';
$proxy_port = '80';

On a Mac you can use SLBC or MacPerl to make the change. If you want to use SLBC then install it first, see the README for information on obtaining and installing SLBC. Then start SLBC up without dropping any files on it. It will display a window that says return to quit, but do not hit return but rather go to the file menu of MacPerl (SLBC is MacPerl with the Search Launcher perl script loaded) and then open the new script, make the necessary changes (unless it has already been changed using another method) and then do a 'save as' and save the modified script under some name, as a runtime. You can also use MacPerl if you already have it installed or want to obtain it here. Just startup MacPerl, open the script, make any necessary changes, then save it as a droplet.

BEAUTY post-processing using the Search Launcher Batch Client version 2.0. provides the summary figure and hypertext links to additional information for most BLASTP and BLASTX search results, including text formatted results returned by the NCBI's BLAST server or produced by the NCBI's BLAST Client.