Whats New 8

• INTRODUCTION
• DATA UPDATES
• NEW AND ENHANCED PROGRAMS
  • Display
  • Sequence Exchange
  • Database Maintenance
• CORRECTED PROGRAM ERRORS
  • Editing
  • NewFeatures
  • Database Searching
  • EQuickIndex
  • Display
  • EPublish
• GRAPHICS
• SYSTEM UTILITIES

WHAT'S NEW IN VERSION 8.1-UNIX OF THE EGCG EXTENSIONS TO THE GCG PACKAGE

January 1995

INTRODUCTION

This document describes changed software features between the initial Version 8.1-UNIX and the current version of the EGCG extensions to the GCG Sequence Analysis Software Package. These software update notes are intended for all EGCG and GCG users and system managers. Read these notes before you install or use Version 8.1-Unix.

You'll find the following information in this document:

- Data Updates. A list of updated data files.

- New and Enhanced Programs. An explanation of new and enhanced programs.

- Corrected Program Errors. Problems and errors corrected since the alpha test of Version 8.0 was first released.

- Graphics. Corrected graphics problems.

- System Utilities. Updates to the system utilities.

DATA UPDATES

Since the original release, we provide new versions of the following data files:

NEW AND ENHANCED PROGRAMS

The latest Version 7.2 includes both new and enhanced programs. These programs include the following:

- Display: EPublish

- Sequence Exchange: ToEmbl

- Database Maintenance: DbStats

Display

The EPublish program has been extended to display the translation of the second sequence in 1 or 3 letter code, using two new menu items.

Sequence Exchange

The ToEmbl programs performs a similar function to ToGenBank, by extracting one or more entries from the EMBL database, and recreating the original EMBL flat file format.

Database Maintenance

DbStats program now supports the command line option -LISTsize which asks for a listing of the n longest entries to be written to the output file in FOSN format.

DbStats also now uses the standard GCG sequence naming convention, instead of asking for the names of database .seq files. The source code of the old version is still included in the distribution under the name of XDbStats, but is not normally built.

CORRECTED PROGRAM ERRORS

All program errors and problems described below have been corrected in the latest Version 8.1. You'll find modified programs described under their respective section as they are found in the EGCG Program Manual.

Editing

NewFeatures

Problem: When you specified -translate it was not correctly interpreted by the program.

Update: The -translate qualifier is now interpreted as described in the documentation for NewFeatures. Note that this is not the standard behaviour of the qualifier in other GCG/EGCG programs, as NewFeatures has to be able to cope with multiple translation tables and cannot use the standard GCG procedure calls.

Problem: When you specify 3-letter codes to be displayed with the THREE command, the program could crash unpredictably.

Update: The problem has been traced and corrected.

Database Searching

EQuickIndex

EQuickIndex did not correctly calculate the map section size on Alpha systems. This has been corrected.

Display

EPublish

The command line interface for EPublish did not correctly recognise the -INfile qualifiers. This has been corrected.

GRAPHICS

The following changes have been made to graphics handling in EGCG programs.

SYSTEM UTILITIES

The following changes have been made to the EGCG system utilities.

Printed: April 22, 1996 15:56 (1162)