select Program S E L E C T Extracts sequences from PIR database Author: G. J. Barton (1990) Maximum Allowed Sequence Length: 8000 Maximum Allowed Number of Sequences: 2000 Enter name of file containing SCORE ID pairs: sh2.top15 Opening File: sh2.top15 Opening File: /data/pir/pir38.seq Just Extract Identifiers/titles (no sequences) ?[Y/N]: Enter Output Filename: sh2.top15.seq Opening File: sh2.top15.seq Searching for: 15 Sequences 1 A34104 2 A43610 3 B34104 4 OKFVYR 5 S15582 6 S20676 7 S20808 8 TVCHS 9 TVFV60 10 TVFVMT 11 TVFVPR 12 TVFVR 13 TVFVS1 14 TVFVS2 15 TVHUSC Found: S20676 1 Found: S20808 2 Found: S15582 3 Found: A34104 4 Found: B34104 5 Found: A43610 6 Found: TVHUSC 7 Found: TVCHS 8 Found: TVFV60 9 Found: TVFVMT 10 Found: TVFVPR 11 Found: TVFVR 12 Found: OKFVYR 13 Found: TVFVS2 14 Found: TVFVS1 15 Extracted: 15 Sequences
You have supplied the name of the file containing score, id pairs (sh2.top15) then the name for a file to save the sequences to (sh2.top15.seq), select then lists the identifiers it is searching for and as they are found in the database, it lists them to the screen again. The sequences are saved in the output file in the same order as they are shown in the sh2.top15 file.
If you have access to a more sophisticated database program, then you may prefer to use that to extract the sequences. For example, the program ``sortsco'' works much faster than ``select'' since it makes use of indexing - See Section 6.3.3 for details.
If you have not set the environment variables for the database file, then the program ``select'' will prompt you for the database filename.