GrailEXP Frequently Asked Questions (FAQ) v1.2

http://compbio.ornl.gov/grailexp/

Introduction
The Exon Prediction Program (Perceval)
The Gene Message Alignment Program (Galahad)
The Gene Assembly Program (Gawain)
CpG Island and Repetitive Element Prediction (Perceval)
Syntax for Command-Line GrailEXP
Installation and Customization of GrailEXP

Introduction

What is GrailEXP?
Who developed GrailEXP?
How is GrailEXP used?
Why should I use GrailEXP?
What is the difference between Grail and GrailEXP?
How is GrailEXP structured?
How does GrailEXP compare to other tools?
Can I access GrailEXP online?
Where do I send bug reports/comments/questions?
Are there any references for GrailEXP?
How do I obtain GrailEXP?

The Exon Prediction Program (Perceval)

What is Perceval?
What are Grail Exon Candidates?
How are Grail Exon Candidates predicted?
How does the program handle repetitives?
What is the pretty output format?
What is the raw output format?
What is the Genome Channel output format?
What is planned for future versions?

The Gene Message Alignment Program (Galahad)

What is Galahad?
What is a gene message alignment?
What databases are searched by the program?
How are gene message alignments calculated?
How does the program handle repetitives?
How does the parallel version work?
What are the advantages of using Blast?
What are the disadvantages of using Blast?
How does the program deal with repeating genes?
How does the program handle short exons?
Can I align just one cDNA with one genomic sequence?
Can I use exons from other exon prediction programs such as Genscan?
Do I have to use exons as seeds or can I align with the whole sequence?
How does the program compare to other EST alignment tools?
What is the pretty output format?
What is the raw output format?
What is the Genome Channel output format?
What is planned for future versions?

The Gene Assembly Program (Gawain)

What is Gawain?
Do I need Grail Exon Candidates AND alignments?
How does the algorithm work?
How does the alternative splicing recognition work?
How does the program locate 5' and 3' untranslated regions?
Can the program recognize pseudogenes?
How do the polya and promoter algorithms work?
What is the difference between open and closed ends?
Can I do single strand gene modeling and when should I do this?
What about ESTs/cDNAs that aren't listed as gene evidence?
What is the pretty output format?
What is the raw output format?
What is the Genome Channel output format?
What is planned for future versions?

CpG Island and Repetitive Element Prediction (Perceval)

How are CpG islands located?
How are simple repeats located?
How are complex repeats located?
What are the advantages of using BLAST?
What are the disadvantages of using BLAST?
How is the sequence masked?
What are the pretty output formats?
What are the raw output formats?
What are the Genome Channel output formats?
What is planned for future versions?

Syntax for Command Line GrailEXP

How do I get version information?
How do I get a list of options?
How do I get a list of available organisms?
How do I request a complete analysis?
How do I specify which output type I want?
How can I specify which strand to analyze?
How do I select the draft sequence genefinder?
How do I request exon candidates?
How do I filter Grail Exon candidates for repetitive elements?
How do I specify my own database of repetitive elements to use?
How do I request gene message alignments?
How do I specify my own BLAST program to use?
How do I specify my own formatdb program to use?
How do I specify which databases to search?
How do I align my sequence with a single cDNA/mRNA/EST?
How do I do a complete alignment (i.e. emulate sim4)?
What does the '--fastalign' option do?
How do I make the search module run in parallel?
How do I specify which machines should do the parallel search?
How do I request gene models?
How do I restrict the alignments to be from one organism?
How do I specify open/closed end gene modeling?
How do I request CpG islands?
How do I request repetitive elements?
How do I obtain a repetitive-masked sequence?
What are some other examples of command line requests?

Installation and Customization of GrailEXP

What are the supported platforms for GrailEXP?
What hardware/software is required to run GrailEXP?
What comes in the installation package?
How do I tell GrailEXP where PERL is located?
What is the GRAILEXP environment variable?
What is the naming convention for executables?
What do I do if GrailEXP says it can't find executables?
How do I set up blastall and formatdb?
How do I change the timeout on blastall?
How do I install a repetitive element database?
What is REPBASE and where do I get it?
What do I do if GrailEXP can't find any organisms besides human and mouse?
How do I install a cDNA/EST/mRNA search database?
What is the GrailEXP Database Format (GXPDF)?
Can I use NCBI databases with GrailEXP?
How do I partition the database for parallel search?
Why should I partition the database even if I am not doing a parallel search?
How do I formatdb a single database?
How do I pformatdb a list of databases?
How do I index a single database?
How do I pindex a list of databases?
What is DOTS and where do I get it?
What is the TIGR EGAD transcript database and where do I get it?
What is NCBI Refseq and where do I get it?
What is the Baylor Human Transcript database and where do I get it?
What is the dbEST database and where do I get it?
How do I make parallel search work?
What is ucspi-tcp and where do I get it?
How do I compile and install tcpclient/tcpserver?
How do I start up the parallel servers?
How do I know if everything is working?

The author and maintainer of this FAQ is Doug Hyatt (hyattpd@ornl.gov). This FAQ applies to GrailEXP version 3.2, released February, 2001. This FAQ was last updated February, 2001.