A DNA editor for an Apple II is described which contains many additional functions apart from just editing sequences. The data files are normal ASCII text or binary files and can thus be used easily by other programs. The program supports a special keyboard which greatly facilitates typing of DNA sequences. Furthermore a speech synthesizer is supported by the editor. The speech feedback, together with the special keyboard, reduces typing errors to a minimu

Bürglin, Thomas R.

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CAB I OS Vol.2, no.2. 1986Pages 99-101SEQGEL: a versatile and comfortable DNAeditor which supports a special keyboard and aspeech synthesizerThomas R.BurglinAbstractA DNA editor for an Apple II is described which contains manyadditional Junctions apart from just editing sequences. The datafiles are normal ASCII text or binary files and can thus be usedeasily by other programs. The program supports a special key-board which greatly facilitates typing of DNA sequences.Furthermore a speech synthesizer is supported by the editor.The speech feedback, together with the special keyboard,reduces typing errors to a minimum.IntroductionIt is obvious that only larger computer systems can handle theincreasing number of DNA and protein sequences, allowingsearches of data banks with reasonable speed. However, simpletasks like entering a sequence do not require fast CPUs andrather block the terminals for other uses. Low-cost personalcomputers can perform such tasks very well.In our institute DNA sequences were usually compiled onpaper before they were typed into the computer. Thus muchtime was spent in writing and proofreading the sequences. Ob-viously a more attractive and convenient editing system for se-quences was needed.None of a collection of programs (Soil and Roberts, 1984)offered such a program for an Apple II system, so a flexibleDNA editor program was written. The data format is compat-ible with the programs by Staden (1977). The data files canalso be used directly or after one conversion with other publish-ed programs for the Apple II (Larson and Messing, 1982;Paollela, 1985; Dardel, 1985).Two low-cost hardware devices which are supported by theprogram improve the speed and reduce the error rate whenentering sequences. One is a special keyboard with onlyT,C,G,A and some additional keys. The second feature is aspeech synthesizer.System and methodsHardwareThe program was written on an Apple He and uses the follow-Department of Cell Biology, Biocenter of the University of Basel, CH-4056 Basel,SwitzerlandPresent address: Department of Biological Chemistry, UCLA School of Medicine,Los Angeles, CA 90024, USAing peripherals: 80 column card; two disk drives; one EPSONFX-80 printer with EPSON parallel interface (slot 1); oneBROTHER daisy-wheel printer with EPSON parallel interface(slot 2); SUPER-SPEECH speech synthesizer (slot 7) (obtain-ed from ECKL Electronic, Erlenmeyerstrasse 3, D-6204Taunusstein 4, FRG for ~ $60). For data transfer a Super SerialInterface is installed and linked to a VAX. However, not allthe peripherals need be present. The minimal requirement isan Apple 11+ or Apple lie with two disk drives. Some func-tions in the PRINT section of the program have to be modified,depending on the connected peripherals.For convenient typing a special keyboard was designed whichcontains only the necessary characters for entering a DNA se-quences and some additional keys for easy editing (Figure 1).The keyboard is connected in parallel with the Apple keyboard.Figure 2 shows which lines have to be used for connecting thekeyboard.Language and data filesThe main program is written in APPLESOFT BASIC. Time-consuming operations are written in 6502 machine code. Theprogram runs under DOS 3.3. The data files created by theprogram are either text files with a carriage return after every60 characters or binary files without any intervening charactersin the sequence. When reading in text files, the program willremove any control characters and convert most of the specialcharacters to a ' —'.A version running under PRODOS is also available. The datafiles created are only text files without any interveningcharacters. However, other text files containing controlcharacters can be read. The sequences in all the data files arenormal ASCII characters. No header or other control informa-tion is present.The program can also create text files (so called CATALOGfiles, similar to the FILE of FILES described by Staden, 1977),which contains the filenames of sequences. Thus it is possibleto keep lists of related sequences.Sequences up to 12400 characters can be handled by theprogram.Program descriptionThe program uses the 40 column screen for better visibility ofthe characters. The screen is split into two parts. The top parthas four lines as a header: the current position (C.P.) and length© IRL Press Limited, Oxford, England 99T.R.Burglin2 •4 a6 a8 a10 a12 a14 a16 aIB a20 a22 a24 a26 a• 1a 3a 5a 7a 9a 11a 13a 15a 17a 19a 21a 23a 25T:C:G:A:*- *—;— * •18-234 - 2 010- 161 - 1612- 1721-2217-223 -7Fig. 2. Scheme of the keyboard plug with numbering for the Apple He. Thenumbers shown have to be connected to the corresponding key.are displayed at the top. Then there is a window of the sequencefrom -15 to +15 of the c.p. The next line is for entering com-mands. The bottom part is a normal scrolling screen.The following commands are available:E (ENTER/OVERWRITE MODE) for entering and editinga sequence.I (INSERT MODE) for insert characters.V (VERIFY MODE) for verifying a sequence.D (DELETE) for deleting within a specified range.DS (DELETE START) marks the start position of a sequencerange to be deleted.DE (DELETE END) marks the end position of a sequencerange to be deleted.L (LIST) lists the sequence on the screen.P (PRINT) prints the sequence.TRANS (TRANSLATE) translates a DNA sequence intosingle-letter amino acid code on disk.G (GO TO) jumps to the specified position in the sequence.T (TOP) jumps to the beginning of the sequence.B (BOTTOM) jumps to the end of the sequence.F (FIND) searches for a specified string.COM (COMPLEMENT) complements the sequence.PASCALMESSING DNAPROGRAMSVAXP R O T O P A S ^^ P A S T O P R O:=;5^:;GETDOSG E T P A T ^PRODOSI—3TEXT FILES t = .PRODOSUSER'S DISIAPPLEWORKSSEOGEL EDITOR~ g TEXT FILES ' ' APPIF WRITERL^FDRFl FO|TOPBINARY FILES t = ! - PAOLEllA DMAPROGRAMSDOS 3.3Fig. 1. Picture of the special keyboard with T.C.G.A the arrows for movingback and forth in the sequence, the dash for unknown nucleotides and the 'OPEN-APPLE' key, which gives double functions to the other keys. It is - 1 3 cm wide.Fig. 3. The scheme illustrates how the different programs and operating systemsrelate to each other.REV (REVERSE) inverts the sequence.RC (REVERSE COMPLEMENT) reverse complements thesequence.NOERR (NO ERROR) replaces all small letter nucleotides(used to indicate uncertainties) with their capital counterparts.SP (SPEECH) switches the speech on and off. When speechis on, the following sounds will be generated: T, C, G, A,X for ' —', uncertain nucleotides will be preceded by aMAYBE. Mismatches and errors will cause a MISTAKE.NEW (NEW) for entering a new sequence.EX (EXIT).Commands for the floppy disk:CATALOG makes a list of all files on the disk.SAVE saves the file (sequence) on disk.LOAD loads the file into the computer memory.APPEND joins two sequences.DELETE deletes a disk file.LOCK protects a disk file from deletion.UNLOCK deprotects a disk file.CFLIST (CATALOG FILE LIST) list the Catalog file.CLR (CLEAR) clears the filenames in memory.In the ENTER, INPUT and VERIFY modes one can use thenormal and the special keyboard for entering and checking se-quences. With the arrows you move back and forth throughthe sequence. Pressing 'open-apple' together with T, C, G orA produces lower case letters which can be used for represen-ting uncertain nucleotides. 'Open-apple' together with the ar-rows moves you automatically through the sequence. While youare in these command modes, you always get speech feedback.The PRINT section allows you to print the sequences invarious formats onto printers or disk (for word processing)either as single-stranded, double-stranded or translated version.DiscussionThe DNA editor described here is fast and convenient to usedue to the command structure and the machine languageroutines. In addition, no reloading of sequences or program100A fast DNA editor using a speech synthesizerparts is necessary when different functions are used. The for-mat of the data files was chosen so that many other programscan use them. The binary files created by the program can beused directly by the programs described by Paolella (1985).The text files can be used with the programs of Dardel (1985).Alternatively they can be converted to PASCAL, where theycan be used with programs described by Larson and Messing(1982) or with a modified version of the programs describedby Malthiery et al. (1984). Furthermore, they can be transfer-red to a VAX computer where they can be used with the pro-grams described by Staden (1977).Apart from the fact that the text files can be used directlyin word processors like APPLEWRITER or APPLEWORKS,the print option allows printing onto the disk. Thus sequencescan be transferred to word processors in numbered and trans-'lated versions, which eliminates another source of error. Figure3 shows how the files and operating systems are related.The use of the character ' — ' for unknown nucleotides is ac-cording to Staden (1977). It is generally accepted because ofits better visibility than 'N' in sequences (Cornish-Bowden,1985). The uncertainty codes used by Staden (1977) are usefulfor computer programs, but hard to remember. The use of lowercase letters for uncertain nucleotides as used in this programis not standard. However, the significance of the small lettersis obvious and they are easily detected in printouts. They area reminder that there are uncertainties in this region of the se-quence which have to be checked.The special keyboard described offers a convenient way oftyping in sequencing gels directly. The convenience is certain-ly similar to digitizing tablets which have been described forother programs (Soil and Roberts, 1984), but the costs are muchlower. In addition, the keyboard is also very convenient fortyping in printed sequences.The program supports a speech synthesizer. This is extremelyvaluable for initial entering as well as for checking of sequences.The computer speaks the sequence, while a single person cancontrol it on a gel or listing. Because the main part of the pro-gram is written in BASIC, modifications for other printers orspeech synthesizers should be easy.AcknowledgementsI would like to thank Jiirg Wenger and Paul Henz for building the keyboard,and Bernard Jacq, Erich Frei and Denice Smith for critical reading of themanuscript.ReferencesCornish-Bowden,A. (1985) Nomenclature for incompletely specified bases innucleic acid sequences: recommendations 1984. Nucleic Acids Res., 13,3021-3030.Dardel,F. (1985) PEGASE: a machine language program for DNA sequenceanalysis on Apple II microcomputer using a binary coding of nucleotides.CABIOS, 1, 19-22.Larson,R. and Messing.J. (1982) Apple II software for M13 shotgun DNAsequencing. Nucleic Acids Res., 10, 39 — 50.Malthiery,B., Bellon.B., Giorgi.D. and Jacq.B. (1984) Apple 11 Pascal pro-grams for molecular biologists. In S6I1.D. and Roberts.R.J. (eds). Vie Ap-plications of Computers to Research on Nucleic Acids II, Pan 2. IRL Press,Oxford. UK, pp. 569-579.Paolella,G. (1985) A fast DNA sequence handling program for Apple II com-puter in BASIC and 6502 assembler. CABIOS, 1, 43 -49 .S6I1.D. and Roberts,R.J. (1984) The Applications of Computers to Researchon Nucleic Acids II, Part 2. IRL Press, Oxford, UK, 428 pp.Staden,R. (1977) Sequence data handling by computer. Nucleic Acids Res.,4. 4037-4051.Received and accepted on 10 March 1986Circle No. 9 on Reader Enquiry Card101

SEQGEL: a versatile and comfortable DNA editor which supports a special keyboard and a speech synthesizer

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