ZSEQ: an interactive DNA sequence analysis program designed for
Contents
1. GLOLZLOISG PH9E6H SLOL 9 Z L 4Pd ajo1e suesOOSWAaYoOIG LUOO ssesdpue yOd SdyjY WO papeojuMoq2. beginning The format for giving sequence positions is From To Qualifier Normally From is less than To and the Qualifier is blank If From is equal to To a single base at that position is specified If From is downstream relative to To and the qualifier is C the complementary strand is specified These conventions follow the EMBL manual When specifying sequence positions at the terminal the entries may be separated by spaces or commas The abbreviations full stop and asterisk are available to represent the current cursor position and the end of the sequence respectively The input FT lines have to be in the fixed format specified by the EMBL manual Otherwise the sequence positions are read in the same way as from the terminal In addition an FT key name Appendix A of the EMBL manual may be selected The key name may be typed in upper or lower case letters Lower case will be converted to upper case by the program Note that in EMBL files the key name has to be in upper case To step through the FT lines is typed at the terminal Typing N starts a new output entry and typing adds results to the previous output Counting Programs are available to count bases to count overlap ping doublets to count overlapping triplets and to count non overlapping triplets to give codon frequencies In manual mode typing accumulates sums of sums unti
3. the first two symbols in a line indicating its type An entry is identified by its ID line which carries a unique eight letter identifier Information lines follow particularly notable being the FT lines which locate the features of importance such as exons and introns The start of the sequence itself is after the SQ line and the entry is terminated by the line Input files to ZSEQ may contain multiple ID entries so that automatic processing of many sequences is made possible The option is also provided to select individual ID entries from a file containing many sequences ZSEQ will also work on an input file containing a sequence alone or will extract multiple sequences from input files in SEQ or GENBANK formats It will not convert the GENBANK sequence positions into an EMBL features table ZSEQ always verifies the symbols present in sequences and has facilities for alteration of unrecognized symbols to the set defined in Appendix B 2 of the EMBL Manual The symbol may be used to pad aligned sequences note that the symbol hyphen cannot be used for this purpose as it means any of A C G or T The output from ZSEQ will be either sequences in EMBL format suitable for storage on disc for further processing or output suitable for printing ZSEQ is divided by function into four activities 1 Counting counts may be made of bases doublets triplets oligonucleotides of up to six in length and codons 2 Filing output may
4. The inversion operation is limited by the memory size of the machine If this proves to be a problem fragments may be inverted and the concatenated in the appropriate order Listing DNA may be listed with position numbers as a single or double strand Translation in all six reading frames may be added When DNA is listed without translation the standard output has 60 bases per line This may be optionally altered to between 10 and 120 bases per line in multiples of 10 When DNA is listed with translation the line length is 45 bases giving 15 amino acids per line Amino acids may be written in the three letter or single letter codes Pattern finding Patterns of up to 1000 bases may be supplied Patterns may contain ambiguous characters N R Y Matching is one sided unambiguous bases in the pattern not being matched by ambiguous bases in the sequence For example Y in the search pattern will match T C or Y in the sequence whereas Y in the sequence will not be matched to T in the pattern In automatic mode a disk file of sequences in EMBL format is used to input the patterns In manual mode each pattern is input at the terminal as required Up to 80 bases may be typed input being terminated by carriage return If a search for total matches is requested the output is in the form of position numbers Matches in the complemen tary strand are marked by Output from a search for partial matches displays the pattern and the porti
5. be sent to disk for further processing Formatting splicing complementation reverse complementation and translation may be performed 3 Listing sequences may be listed with position numbers as single or double stranded DNA or translated in up to six reading frames 4 Pattern finding partial or total matches to an input pattern may be found in one or both strands When running in automatic mode ZSEQ will process each ID entry in a file from position 1 to the line This allows rapid processing with minimal effort In manual mode each individual ID entry may be selected and then parts of the sequence may be further selected by position Vol 12 numbers If a sequence is specified to be circular reading over the physical end beginning of the sequence may be performed Part of the additional power of ZSEQ over other analysis systems comes from its exploitation of the EMBL features table Selecting the F option in manual mode enables the FT lines to be read by the program The FT lines in the current ID entry are displayed by typing the symbol in response to the prompt for a key name Feature table key names Appendix A of the EMBL manual may be selected to simplify specific tasks For example by selecting the key name CDS gene splicing may be performed with the introns discarded This facility is available in all parts of the package not merely for file output Starting The package is intended to be self documenting I
6. 608th MEETING KEELE Check for updates 1015 ZSEQ an interactive DNA sequence analysis program designed for microcomputers MARTIN J BISHOP Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ U K ZSEQ is a self documenting interactive DNA sequence analysis package designed for small computers based on Z80 microprocessors The SZEQ philosophy is to provide basic operations which can be economically performed on small machines ZSEQ is written in BCPL a language which has been carefully designed to be near optimal for flexible text processing applications Richards amp Whitby Strevens 1979 ZSEQ provides counting listing translating filing splicing and pattern finding facilities ZSEQ does not provide searches for genes secondary structure determina tions nor comparisons of two or more sequences activities which are best carried out on larger machines The only sequence length limitation on the programs is the value of the maximum integer held in one word of the BCPL implementation On the Z80 this is 32766 ZSEQ is designed to work on input files in EMBL format and the program should be used in conjunction with the EMBL Nucleotide Sequence Data Library User Manual EMBL manual Cameron et al 1983 Each entry in the EMBL database corresponds to a single sequence and an entry is structured so that it can be easily read by humans or machines Each entry is composed of lines
7. acters but the words MADEFROM Cidentifier are included on the ID line Any clashes may therefore be distinguished even though they have to be acessed by the same search key Automatic mode Automatic mode is used to process input files containing a large number of ID entries Such files might typically contain homologous genes from a variety of organisms or genes sliced from a single genome using the Filing option in manual mode operating on the EMBL FT lines Terminal output is minimal in automatic mode ID lines being reflected to keep track of processing Sequences are treated as linear molecules and are processed from position 1 to the line of each ID entry 0z0z eunr 6 uo ysanb Aq jpd GLOLZLOISG Pr9E6H SLOL 9 Z L 4Pd ajo1e suesOOSWaYoOIG LUOD sseidpue yOd sdyjY WoO papeojumoq 1016 Manual mode Manual mode is used to process individual ID entries The sequence may be accessed either by position numbers or from the FT lines An ID entry is accessed by giving its short identifier This may be specified in lower case letters which will be converted to upper case by the program Note that EMBL short identifiers must be in upper case If a is typed instead of an identifier a listing of the ID lines in the input file is displayed on the screen The DNA sequence may be treated as a circular molecule or a linear fragment In the former case it is possible to read past the end of the sequence as it appears on paper into the
8. eractive protein sequence analysis package designed for small computers based on Z80 microprocessors ZPEP provides counting listing reverse translating splicing and pattern finding facilities ZPEP does not provide secondary structure determinations nor compari sons of two or more sequences ZPEP is designed to work on input files in EMBL format but will also work on an input file containing a sequence alone or will extract multiple sequences from input files in SEQ or GENBANK formats Input sequences should be in the one letter code for amino acids ZPEP always verifies the symbols present in sequences and has facilities for alteration of unrecognized symbols to the set defined by IUPAC IUB and given in Appendix B 4 of the EMBL Nucleotide Sequence Data Library User Manual EMBL manual Cameron et al 1983 The symbol may be used to pad aligned sequences The output from ZPEP will be either sequences in EMBL format suitable for storage on disc for further processing or output suitable for printing Output may be in the one letter or the three letter code ZPEP is divided by function into four activities 1 Counting counts may be made of amino acids doublets and triplets 2 Filing output may be sent to disk for further processing Formatting splicing and reverse translation may be performed 3 Listing sequences may be listed with position numbers in the one letter or the three letter code with reverse translat
9. ion 4 Pattern finding partial or total matches to an input pattern may be found in one or both strands Counting Programs are available to count amino acids to count overlapping doublets and to count overlapping triplets In manual mode typing accumulates sums of sums until the next N is typed When counting doublets or triplets the deletion character I is ignored If ambiguous characters B Z X are encountered counts involving them are discarded Filing The filing programs take sequences in EMBL format and output altered sequences in EMBL format to disk Selected parts of the sequences may be output In addition reverse translation is available Listing Proteins may be listed with position numbers and reverse translation may be added Vol 12 When proteins are listed without translation the standard output has 60 amino acids per line This may be optionally altered to between 10 and 120 amino acids per line in multiples of 10 When proteins are listed with translation the line length is 20 amino acids giving 60 nucleotides per line Amino acids may be written in the three letter or the single letter code Pattern finding Patterns of up to 100 amino acids may be supplied Patterns may contain ambiguous characters B Z X Matching is one sided unambiguous amino acids in the pattern not being matched by ambiguous amino acids in the sequence For example B in the search pattern will match D N
10. is arranged with a main menu and seven overlay segments Though ZSEQ has been designed for a machine with limited memory it will be easy to implement on any system 1984 0z0z unr 6 uo ysanB Aq Jpd GLOLZLOISA pr9E6P SLOL 9 ZL Pd ejoMNWe sUeNOOSWAYoOIG WOD sseidpuejod sdyY Wo papeojumogq 608th MEETING KEELE for which a BCPL compiler exists It has been implemented unaltered except for a small machine dependent section on an IBM 3081 computer under the MVS operating system On this machine the BCPL word length is 32 bits and ZSEQ will process DNA sequences of length up to 2147483647 bases Because the sequence files are accessed by virtual I O also used on this machine to move arrays in and out of main store the response is very fast 1017 Cameron G Hamm G Nial J Rudloff A Stoesser G amp Stueber K 1983 EMBL Nucleotide Sequence Data Library User Manual European Molecular Biology Laboratory Heidelberg Richards M amp Whitby Strevens C 1979 BCPL the Language and its Compiler Cambridge University Press Cambridge Staden R 1979 Nucleic Acids Res 6 2601 2610 Wilson I D amp Webster C A 1980 Z80 BCPL System for CP M and CDOS F Fretwell Downing Ltd Sheffield ZPEP an interactive protein sequence analysis program designed for microcomputers MARTIN J BISHOP Department of Zoology University of Cambridge Downing Street Cambridge CB2 3EJ U K ZPEP is a self documenting int
11. l the next N is typed When counting the base sum the numbers of individual characters A C G T R Y N and Appendix B 2 of the EMBL manual in the sequence are recorded as well as the numbers of purines A G R pyrimidines C T Y and all bases U is treated as T and the lower case letters as their upper case equivalents When counting doublets or triplets the deletion character is ignored If ambiguous characters R Y N are encountered counts involving them are discarded When counting codons the deletion character is ignored and any non overlapping triplet involving ambiguous characters is discarded Oligonucleotides of lengths between four and six bases may also be counted though the output may be voluminous Filing The filing programs take sequences in EMBL format and output altered sequences in EMBL format to disc Selected parts of the sequences may be output In addition complementation inversion and translation oper ations are available This section makes it very straightforward to output the genes from longer sequences using the EMBL FT lines For example by selecting the key name TRNA all tRNA genes may be output By selecting the key name CDS and using the N and controls any type of RNA processing may be undertaken with or without translation BIOCHEMICAL SOCIETY TRANSACTIONS Note that if the qualifier C is set the output sequence fragment is complemented but not inverted
12. n answer to prompts the following should usually have the desired effect for help control Q to quit the current task control C to stop the program Answers to prompts may be in upper or lower case letters Verifydna This section checks for correct EMBL format of the input If the input is not in EMBL format the input is passed to EMBLFORMAT for conversion The sequence is then checked to ensure that it contains only the characters specified in Appendix B 2 of the EMBL manual If there are characters in the input which do not conform to the standard but for which equivalents exist the opportunity is given to convert them A wild selection of characters at this point indicates that some arbitrary piece of text has been read in by mistake Note that the Staden Staden 1979 or other uncertainty codes are not accepted by ZSEQ If the sequences are correct they are output for further processing Emblformat This section converts sequences to EMBL format A sequence without other information is converted by the addition of an ID line CC lines FH line FT lines SQ line and line Sequences is GENBANK or SEQ format are auto matically converted to EMBL format so that they may be processed by the program However the GENBANK positional information is not converted to a feature table Identifiers in GENBANK or SEQ files may be up to 10 characters long On conversion to EMBL format identifiers have to be truncated to eight char
13. on of the sequence with matches marked by colons Circular sequences have to be declared in manual mode in order that the physical end beginning of the sequence may be searched Negative position numbers mark the start of the match near the physical end of the sequence Thus 2 is the position three bases before the end of the sequence Translation Translation is available in both the Filing and Listing sections The nuclear or mammalian mitochondrial codes are provided In addition the user may alter either of these to the code table appropriate for other sequences All that is necessary is to type the codons and the altered amino acid symbols which they represent Translated output may be in one letter Dayhoff or three letter codes Codons involving ambiguous base symbols R Y N are always translated if possible otherwise the symbol X Xxx is output Note that the aspartic and glutamic uncertainties are translated as X When translating a gene with codons which are internally split by introns it is necessary to first output the DNA of the coding region and then to translate it The translation programs do not automatically take care of this situation Implementation ZSEQ has been implemented under a 64K CP M operating system using the BCPL compiler described by Wilson amp Webster 1980 and supplied by F Fretwell Downing Ltd The executable code should run on any machine which has the CP M operating system The package
14. or B in the sequence whereas B in the sequence will not be matched to D in the pattern In automatic mode a disk file of sequences in EMBL format is used to input the patterns In manual mode each pattern is input at the terminal as required Up to 80 amino acids may be typed input being terminated by carriage return If a search for total matches is requested the output is in the form of position numbers Output from a search for partial matches displays the pattern and the portion of the sequence with matches marked by colons Reverse translation Reverse translation is available in both the Filing and Listing sections The nuclear or mammalian mitochondrial codes are provided In addition the user may alter either of these to the code table appropriate for other sequences All that is necessary is to type the codons and the altered amino acid symbols which they represent Reverse translated output contains the Staden uncertainty codes Staden 1979 R for A or G Y for C or T 5 for A or C 6 for G or T 7 for A or T 8 for G or C for A or C or G or T or any three out of the four Ambiguous amino acids B Z X are not translated but the symbols are output Cameron G Hamm G Nial J Rudloff A Stoesser G amp Stuber K 1983 EMBL Nucleotide Sequence Data Library User Manual European Molecular Biology Laboratory Heidelberg Staden R 1979 Nucleic Acids Res 6 2601 2610 0z0z eunr 6 uo s nb Aq ypd
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