kristoff@NET.BIO.NET (Dave Kristofferson) (08/03/89)
BIONET is pleased to announce the availability of the Multiple Aligned Sequence Editor (MASE) on the Sun system. MASE was developed at the MBCRR (Molecular Biology Computer Research Resource by Dr. Jerzy Jurka and Donald Faulkner and was then further enhanced during Dr. Jurka's stay at BIONET. We had hoped to make it available to the entire community, but due to our current unfortunate circumstances the editor will only be accessible to our beta users during our remaining two months on-line. MASE only runs on the Sun system and not on the DEC 2065. MASE can accept initial multiple sequence alignments produced by the IntelliGenetics GENALIGN program WRITE command. These alignments can then be adjusted manually in the MASE editor. I include the Sun help file below which briefly describes the editor. The editor can be obtained free of charge from the MBCRR as indicated in the help file below. Sincerely, Dave Kristofferson BIONET Resource Manager kristoff@net.bio.net or kristofferson@bionet-20.bio.net ---------------------------------------------------------------------- MASE - Multiple Aligned Sequence Editor (last update 8/2/89) Dear Colleagues, Thanks to the courtesy of BIONET, we present you with a powerful sequence editor (MASE) which may be useful in your everyday work. A brief description of the editor appeared in Trends in Biochemical Sciences 13:321-322(1988). The editor can be acquired free of charge from Susan Russo, MBCRR, Dana-Farber Cancer Institute, 44 Binney Street, Boston MA 02115, USA. Tel. (617)732-3746. MASE was developed originally at the Molecular Biology Computer Research Resource at Dana Farber and additional enhancements were made in collaboration with BIONET. This brief note gives only a short guide on how to get started. 1. Take any sequence file in IntelliGenetics format. If you want to align multiple sequences, the easiest thing is to keep them in the same file although you can also load additional files using the ":LOAD" command in the editor. Let the filename be: "anysequence". 2. Enter "mase anysequence" at the bionet% prompt. You are in the editor. If your input file contains many sequences they will show up one under another on the screen with LOCI NAMES (sequence names) on the left hand side. MOVING THE CURSOR If your sequences are long or their number is large you can move around to see them: (1) from top to bottom - type the desired number followed by "j" (2) from bottom to top - type the desired number followed by "k" (3) from left to right - type the desired number followed by "]" (4) from right to left - type the desired number followed by "[" You can also jump to any specified position if your number is followed by "J" (capital J). At this point you will learn that MASE has two independent windows which can be put side by side by typing ":synchronize windows" followed by return. ALIGNMENT If you want to align your sequences, you can shift one sequence against another by typing "i" (this inserts the alignment gap: '-' at the position of the cursor). You can also pre-align your sequences using the IntelliGenetics GENALIGN program. The "Write" command in GENALIGN automatically puts GENALIGN output in MASE input format. However, it uses a "?" instead of a "-" as the symbol for alignment gaps. You can replace "?" by "-" using an editor such as Emacs (use Esc-X replace-string<cr>) or the UNIX "tr" command. Example: tr '?' '-' <input file >output file (from genalign) (to MASE) COMMAND MODE You can use over 100 different MASE functions. They are displayed after you type ":" and use the down arrow to select them. They also show up after you type the first few letters of the command as in the case of ":synchronize windows". You need only type ":sy". You can see a brief description of each command by typing "?" while the command is displayed on the screen. OUTPUT FILE Once you are through with your alignment, you may want to generate an output file. There is a command ":OUTPUT FILE" which guides you through this process. You also may use ":SET VARIABLE" and the down arrow key to select and change parameters determining the desired output format. HOW TO FINISH MASE is very friendly in this respect. You can always use the immortal ctrl-C followed by return to abort any command. If you ctrl-C again MASE asks you if you want to exit. You can also use the ":QUIT" command. We will volunteer our assistance to all who are hopelessly lost during their first steps. Send your questions to mase@net.bio.net where they will be answered by one of the program's authors. The editor can be acquired from Susan Russo at the address above (see also the TIBS paper). Good luck and have fun! Don V. Faulkner Jurek Jurka (yurek yurka)