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VARIANT: a store and retrieval system for human haemoglobin variants
Computer Methodr and Programs in Biomedicine, Elsevier
113
31 (1990) 113-114
COMMET 01070
Section II. Systems and programs
VARIANT: a store and retrieval system for human haemoglobin variants M.F.
Macchiato
’ and A. Tramontano
2
’ Dipartimento di Scienze Fisiche, Naples, Italy, and ’ European Molecular Biology Laboratory, Heidelberg F.R. G.
VARIANT, a FORTRAN 77 computer system for storing and retrieving the ammo acid replacements in human haemogfobin variants on a multicriterion basis, is presented. The system is transportable and user-friendly, can easily be expanded and can also be used to create a database of the amino acid replacements in families of homologous proteins, becoming an efficient tool for evolutionary studies. VARIANT;
Hemoglobin variants, human; Amino acid replacement; Database
The work of our group centers around thermodynamic and statistical characteristics of DNA and protein sequences. Such activity requires suitable tools for the manipulation, handling and analysis of data; thus, several computer programs have been developed and made available [l-3]. We are now interested in the study of amino acid replacement in human haemoglobin variants [4], and have designed and implemented a store and retrieval system which allows the user to insert and recover data on these variants. The selection criteria are: names of the variant, protein chain, mutation (wild-type amino acid, replacing amino acid and position of the mutation), reference (authors, journal and year) and comment. Even though we plan to use the system for the haemoglobin variants, it can obviously be used to create a database of any kind of amino acid replacements, including the evolutionary dif-
Correspondence: M.F. Macchiato, Dipartimento di Scienze Fisiche, Mostra d’Oltremare, Pad. 20, 80125 Naples, Italy. 0169-2607/90/$03.50
ferences in families of homologous proteins, since more than one mutation can be stored for each entry. The database logical structure has been designed in order to satisfy most data retrieval questions that various users might ask. The available commands of the VARIANT system are the following. Insertion commands: INSERT (insert a new variant in the database). Retrieval commands: NAME (retrieves by variant name), CHAIN (retrieves by chain name), WT (retrieves by wild-type amino acid name), MUT (retrieves by replacing amino acid name), POS (retrieves by position of the variant), AUTH (retrieves by author name), JOURNAL (retrieves by journal name), YEAR (retrieves by year of publication, > year, =year,
0 1990 Elsevier Science Publishers B.V. (Biomedical Division)
114
The syntax of all commands, and QUIT, is:
except INSERT,
HELP
command/modifier”user-supplied string” The
possible modifiers
are /OUTPUT,
/SAVE,
/LIST.
Nine retrieval commands are provided to get information on a variant. Each variant in the database is an entry and contains several fields which can all be used to retrieve it. Multiple names, references, comments and mutations are allowed for each entry. The fields and their size limits are: NAME (3, lo), CHAIN (1, 15) UT (100, 3), MUT (100, 3), POS (100, 3), AUTH (3, 20), JOURNAL (3, 80), YEAR (3, 4), COMMENTS (10, SO), where the first number in parentheses is the number of alternative fields and the second is the size (characters). The number of alternative values of each field and their size can easily be changed since they are contained in a separate file which can be edited by the user. The INSERT command allows the store a new variant in the database. When the user types the INSERT command, he is interactively prompted for each field of the entry. When alternative values are allowed for a field, the system repeats the prompt until the maximum number of alternative fields is reached or until the user types a blank line. At any time the insertion can be avoided by typing the character *. There is no software limitation on the size of the database. All the commands can access user-preselected entries. In fact if the /SAVE modifier follows a
command, the system will create an internal list containing only the selected entries. Later on, the user can give a different command followed by the /LIST modifier and the search will be limited to the entries in the internal list. An on-line help facility is available. It gives information on the structure of the entry in the database and on the available commands. The syntax for HELP is: HELP or HELP ’ ’ command ’ ’ In the first case general information on the system is given, in the second the syntax and use * are displayed. of * ’ command. All the commands can be followed by the modifier /OUTPUT = f i lename which copies the selected entries to the external file filename. The QUIT command closes the session and deletes the internal list, if any. The source code and the user manual of the program are available upon request, and free of charge.
References [l] G. Piemo, N. Bami, M. Candurro, A.M. Fran&, L. Iuliano, M.F. Maccbiato, G. Mastrocinque, C. Moscatelli, V. Scarlato, A. Tramontano and A. Cascino, Nucleic Acids Res. 12 (1984) 281. [2] A. Tramontano and M.F. Macchiato, Comput. Biol. Med. (1987) (in press). [3] C.J. Rawlings, Software Directory for Molecular Biologists, Stockton Press, U.S.A. (1986). [4] W.P. Winter (ed.), Haemoglobin Variants in Human Population (Howard University, Washington, DC, 1986).
113
31 (1990) 113-114
COMMET 01070
Section II. Systems and programs
VARIANT: a store and retrieval system for human haemoglobin variants M.F.
Macchiato
’ and A. Tramontano
2
’ Dipartimento di Scienze Fisiche, Naples, Italy, and ’ European Molecular Biology Laboratory, Heidelberg F.R. G.
VARIANT, a FORTRAN 77 computer system for storing and retrieving the ammo acid replacements in human haemogfobin variants on a multicriterion basis, is presented. The system is transportable and user-friendly, can easily be expanded and can also be used to create a database of the amino acid replacements in families of homologous proteins, becoming an efficient tool for evolutionary studies. VARIANT;
Hemoglobin variants, human; Amino acid replacement; Database
The work of our group centers around thermodynamic and statistical characteristics of DNA and protein sequences. Such activity requires suitable tools for the manipulation, handling and analysis of data; thus, several computer programs have been developed and made available [l-3]. We are now interested in the study of amino acid replacement in human haemoglobin variants [4], and have designed and implemented a store and retrieval system which allows the user to insert and recover data on these variants. The selection criteria are: names of the variant, protein chain, mutation (wild-type amino acid, replacing amino acid and position of the mutation), reference (authors, journal and year) and comment. Even though we plan to use the system for the haemoglobin variants, it can obviously be used to create a database of any kind of amino acid replacements, including the evolutionary dif-
Correspondence: M.F. Macchiato, Dipartimento di Scienze Fisiche, Mostra d’Oltremare, Pad. 20, 80125 Naples, Italy. 0169-2607/90/$03.50
ferences in families of homologous proteins, since more than one mutation can be stored for each entry. The database logical structure has been designed in order to satisfy most data retrieval questions that various users might ask. The available commands of the VARIANT system are the following. Insertion commands: INSERT (insert a new variant in the database). Retrieval commands: NAME (retrieves by variant name), CHAIN (retrieves by chain name), WT (retrieves by wild-type amino acid name), MUT (retrieves by replacing amino acid name), POS (retrieves by position of the variant), AUTH (retrieves by author name), JOURNAL (retrieves by journal name), YEAR (retrieves by year of publication, > year, =year,
0 1990 Elsevier Science Publishers B.V. (Biomedical Division)
114
The syntax of all commands, and QUIT, is:
except INSERT,
HELP
command/modifier”user-supplied string” The
possible modifiers
are /OUTPUT,
/SAVE,
/LIST.
Nine retrieval commands are provided to get information on a variant. Each variant in the database is an entry and contains several fields which can all be used to retrieve it. Multiple names, references, comments and mutations are allowed for each entry. The fields and their size limits are: NAME (3, lo), CHAIN (1, 15) UT (100, 3), MUT (100, 3), POS (100, 3), AUTH (3, 20), JOURNAL (3, 80), YEAR (3, 4), COMMENTS (10, SO), where the first number in parentheses is the number of alternative fields and the second is the size (characters). The number of alternative values of each field and their size can easily be changed since they are contained in a separate file which can be edited by the user. The INSERT command allows the store a new variant in the database. When the user types the INSERT command, he is interactively prompted for each field of the entry. When alternative values are allowed for a field, the system repeats the prompt until the maximum number of alternative fields is reached or until the user types a blank line. At any time the insertion can be avoided by typing the character *. There is no software limitation on the size of the database. All the commands can access user-preselected entries. In fact if the /SAVE modifier follows a
command, the system will create an internal list containing only the selected entries. Later on, the user can give a different command followed by the /LIST modifier and the search will be limited to the entries in the internal list. An on-line help facility is available. It gives information on the structure of the entry in the database and on the available commands. The syntax for HELP is: HELP or HELP ’ ’ command ’ ’ In the first case general information on the system is given, in the second the syntax and use * are displayed. of * ’ command. All the commands can be followed by the modifier /OUTPUT = f i lename which copies the selected entries to the external file filename. The QUIT command closes the session and deletes the internal list, if any. The source code and the user manual of the program are available upon request, and free of charge.
References [l] G. Piemo, N. Bami, M. Candurro, A.M. Fran&, L. Iuliano, M.F. Maccbiato, G. Mastrocinque, C. Moscatelli, V. Scarlato, A. Tramontano and A. Cascino, Nucleic Acids Res. 12 (1984) 281. [2] A. Tramontano and M.F. Macchiato, Comput. Biol. Med. (1987) (in press). [3] C.J. Rawlings, Software Directory for Molecular Biologists, Stockton Press, U.S.A. (1986). [4] W.P. Winter (ed.), Haemoglobin Variants in Human Population (Howard University, Washington, DC, 1986).