22 Genetic Resources Cloned Genes of Storage Proteins Keith 0. Elliston, Shahid Imran, and Joachim Messing Waksman Institute (K.O.E, J.M.) and Center for Advanced Biotechnology and Medicine (S.I.), Rutgers University, Piscataway, NJ 08855-0759 USA The compilation of the cloned and sequenced plant storage protein genes was performed on Release 14 of the EMBL database (Hamm & Cameron, 1986). This list includes only those genes that have been cloned, sequenced, and submitted to the database. We used the sequence analysis package from the Genetics Computer Group, GCG version 5.1 of Devereux et al. (1984) run on a Digital Systems Vax 11/785 minicomputer. Specifically, the program "Strings" was used to locate all sequences that had the charac- ter string storage or seed in their documentation. All entries that matched the string seed but not storage were checked to see if they were indeed storage protein genes; those that were not were eliminat- ed. The data from this list of sequences was extracted and concate- nated into a single file using the program "Fetch" of the GCG package. The relevant data of interest was then extracted using the program "Features" (written by S.I.), and formatted into a table using the program "make_table" (written by S.I. and K.O.E.). In order to eliminate duplications, the data from Genbank and EMBL databases were cross referenced using the spreadsheet program Excel on a Mac- Intosh SE. Additional searches were done using names of known storage proteins as strings; e.g., zein. This approach can be generalized to formulate lists of any class of genes represented in the EMBL database. We should note that the EMBL database is directly accessible "online" via the Bit- Net computer network. Acknowledgements: The computer analysis was supported by a Grant from the Department of Energy FGO2-84ER13210 to JM. References Hamm, G.H. & G. N. Cameron. 1986. The EMBLdata library. Nuc. Acids Res. 14:5-9. Devereux, J.B., P. Haeberli & O. Smithies. A comprehensive set of sequence analysis program for the VAX. 1984. Nuc. Acids Res. 12: 387-395.

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Page 1: Cloned genes of storage proteins

22 Genetic Resources

Cloned Genes of Storage Proteins Keith 0. Elliston, Shahid Imran, and Joachim Messing

Waksman Institute (K.O.E, J.M.) and Center for Advanced Biotechnology and Medicine (S.I.), Rutgers Universi ty,

Piscataway, NJ 08855-0759 USA

The compi la t ion of the c loned and sequenced p lant s torage pro te in genes was pe r fo rmed on Release 14 of the EMBL da tabase ( H a m m & Cameron , 1986). This list includes only those genes that have been cloned, sequenced, and submit ted to the database.

We used the sequence analysis package f rom the Genet ics C o m p u t e r Group, GCG version 5.1 of Devereux et al. (1984) run on a Digital Sys tems Vax 11/785 min icompu te r . Specifically, the pro- g ram "Strings" was used to locate all sequences that had the charac- ter s t r ing storage or seed in their documen ta t i on . All ent r ies that ma tched the str ing seed but not storage were checked to see if they were indeed storage prote in genes; those that were not were eliminat- ed. The data f rom this list of sequences was extracted and concate- na ted into a single file using the p rog ram "Fetch" of the GCG package. The re levan t data of in teres t was then ex t rac ted us ing the p rog ra m "Features" (wri t ten by S.I.), and format ted into a table us ing the p r o g r a m "make_table" (wri t ten by S.I. and K.O.E.). In o rde r to e l iminate dupl icat ions, the data f rom Genbank and EMBL databases were cross referenced using the spreadsheet p rog ram Excel on a Mac- Intosh SE. Addit ional searches were done using names of k n o w n storage proteins as strings; e.g., zein.

This app roach can be genera l ized to fo rmula te lists of any class of genes rep resen ted in the EMBL database. We should note that the EMBL da tabase is d i rec t ly accessible "online" via the Bit- Net compute r network.

Acknowledgements: The computer analysis was supported by a Grant from the Department of Energy FGO2-84ER13210 to JM.

References

Hamm, G.H. & G. N. Cameron. 1986. The EMBL data library. Nuc. Acids Res. 14:5-9. Devereux, J.B., P. Haeberli & O. Smithies. A comprehensive set of sequence analysis

program for the VAX. 1984. Nuc. Acids Res. 12: 387-395.