Program : PRF2MSEQ
Version : 971111
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : convert profile scan results into multiple sequence alignment
Package : SBIN
Reference(s) for this program:
* 1 * G.J. Kleywegt & T.A. Jones (1998). Databases in protein crystallography. Acta Cryst D54, 1119-1131. [http://alpha2.bmc.uu.se/gerard/papers/databases.html] [http://www.iucr.org/iucr-top/journals/acta/tocs/actad/1998/actad5406_1.html]
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
971023 - 0.1 - first version
971111 - 1.0 - cleaned up code and manual
PRF2MSEQ is a simple non-interactive program which reads a list of profile/sequence matches (calculated with the pftools-program "pfsearch", with the "-y" command-line option) and converts this into a partial multiple sequence alignment of the matching sequences in a format suitable for MSEQPRO (which can be used to generate a new profile based on these aligned sequences).
Usage: PRF2MSEQ < scan_results.file > multi_sequence.file
Typical example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- pfsearch -ry pfx.prf /nfs/scr_uu5/gerard/sprot34.dat > pfx.hits PRF2MSEQ < pfx.hits > pfx.mseq ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a part of an input file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- 1131 pos. 28 - 250 P35694|BRU1_SOYBN BRASSINOSTEROID-REGULATED PROTEIN BRU1. # # P 4 CSXDNWTVADXNGVTTS----------------XSLQLGQITQ-XNVCARYYYMNXYKMF -164 # S 28 CA--GSFYQD-----FDltwggdrakifnggqlLSLSLDKVSGsGFKSKKEYLFG----- -209 # # P 47 HLWXGLYSFDVDPAEQP------XGLNGSFFMGPM-XCCDEMDIEFDNXPHIALNPHXCD -111 # S 76 RID----------MQLKlvagnsAGTVTAYYLSSQgPTHDEIDFEFLG----NLSGD--- -166 # # P 100 SGGCEWNPY--XTGPFS-------------XLDTSKFHTVVFQWDPSXKITRYYQ----X -70 # S 119 -------PYilHTNIFTqgkgnreqqfylwFDPTRNFHTYSIIWKPQ-HIIFLVDntpiR -113 # # P 141 TFPQAXNTLTAXGLANMPKAPXSWMDIMMSLWNGTXFSNPWLD----------------- -27 # S 171 VFKNA-EPLGV----PFPKNQ--PMRIYSSLWNAD----DWATrgglvktdwskapftay -65 # # P 183 -----------------XGAPNDAEXNDAPNTHVVYS -7 # S 220 yrnfkaiefsskssisnSGAEYEAN------ELDAYS -34 # 1231 pos. 64 - 268 P33693|EXOK_RHIME SUCCINOGLYCAN BIOSYNTHESIS PROTEIN EXOK. # # P 4 CSXDNWTVADXNGVTTS-XSLQLGQITQ-----XNVCARYYYMNXYKMFHLWXGLYSFDV -153 # S 64 CT---WSKKQ---VKTVdGILELTFEEKkvkerNFACGEIQTRK---RFGYG--TYEARI -158 # # P 58 DPAEQPXGLNGSFFMGPM----XCCDEMDIEFDN--XPHIALNPHXCDSGGCEWNPYXTG -99 # S 113 KAADGS-GLNSAFFTYIGpadkKPHDEIDFEVLGknTAKVQINQYVSAKGGNEFLAD--V -101 # # P 112 PFSXLDTSKFHTVVFQWDPSXKITRYYQXTFPQA--XNTLTAXGLANMPKAPXSWMDIMM -41 # S 170 PGG--ANQGFNDYAFVWEKN-RIRYYVN-----GelVHEVTD--PAKIPVNA---QKIFF -54 # # P 170 SLWNGTXFSNPWLD-------------------XGAPNDAE--------XNDA -15 # S 217 SLWGTD-TLTDWMGtfsykeptklqvdrvaftaAGDECQFAesvacqleRAQS -2 # ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Example of a part of an output file:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! 1131 pos. 28 - 250 P35694|BRU1_SOYBN BRASSINOSTEROID-REGULATED PROTEIN BRU1. CA GSFYQD FD SLSLDKVSG FKSKKEYLFG RID MQLK GTVTAYYLSSQ THDEIDFEFLG NLSGD PY TNIFT DPTRNFHTYSIIW ! 1231 pos. 64 - 268 P33693|EXOK_RHIME SUCCINOGLYCAN BIOSYNTHESIS PROTEIN EXOK. CT WSKKQ VKTV ILELTFEEK FACGEIQTRK RFGYG TYEARIKAADGS GLNSAFFTYIG PHDEIDFEVLG AKVQINQY SAKGGNEFLAD VPGG ANQGFNDYAFVW ! 2317 pos. 40 - 236 P07980|GUB_BACAM BETA-GLUCANASE PRECURSOR (EC 3.2.1.73) (ENDO-BETA-1,3-1,4 GLUCANASE) (1,3-1,4-BETA S DGYSNGD NNVSMT EMRLALTSP FDCGENRSVQ TYGYG LYEVRMKPAKNT GIVSSFFTYTG PWDEIDIEFLG TKVQFNYY NGAGNHEKFAD LG DAANAYHTYAFDW ! 1971 pos. 41 - 251 P37073|GUB_BACBR BETA-GLUCANASE PRECURSOR (EC 3.2.1.73) (ENDO-BETA-1,3-1,4 GLUCANASE) (1,3-1,4-BETA FYES FD AGVWTN RLTIAKKTT SARNYKAG NDFYHYG LFEVSMKPAKVE GTVSSFFTYTG PWDEIDIEFLG TRIQFNYF NGVGGNEFYYD LG DASESFNTYAFEW ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present ("peppar, peppar").
Does not compute.