perl -e '$a="ATEH...GYS....I..CVNV...FGQ.....RTY.....F.YC.EY....G....D
+....TE....RL...R..E....V.IA..SVG.E.L-.-.---..-----...................
+...........................................................VPE.p-RTP.
+Y.A..M.S..V.TPA.TK---------.......-........---TS........IYGY.GT.R.P..
+......VP.......D...LQCVSISNWSMAR.......................KI..GE.Y...L..
+LE...-....--..-.....-..--........--...R..GF.P....V..Y................
+.....................................................................
+..............-...-..................................................
+....-.--....---EARV.D.P.L.TRL..V....IDR..RIT.T.............F.........
+..GW.............CS........V.N.......RY..--.----.......-....-.--.....
+.....................................................-...............
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+................-.-.---DW.RH..Q.G...R....S..........ST...C.....D.....
+IEV..D....CD.V.S...DL.V...A..V....P..D..DN.SW.-.......--..-P.L..YRC..
+L.S.F........DI.EC.....M..S..A.D......GG...---FPCAEKP...D.DIV........
+.I.QI..S.CV.CY.ET...G--.----..-Ggsadgaggvgvnggatpaptqshh.............
+.....................................................................
+........................gngesggipyypqaatagvgaqppVFG....R..SG..L......
+.H.....L......F.TI..GT.CDPVG--.....---..-.-...-..-.-----.............
+...---.----...........................EADV..Y..EF--.P....SEY.EL.LLGFM
+L.FFQRY.A..PSFMTGYNI.N...S..FDLKYILTR..L.E......Y..............L-.-.-
+..-..-..--...Y..K........................L.DV.QR.F..C.KVPV..AQGG....R
+FFLHSPT---..-...-LYrRH.Q.....D..RAS.FaaaA.A.NA..P..T.K...............
+V.....Y........IS..G..CV.VVD.MY.PVCM....A....KT.--......N...SP.N.YK.L
+N";if($a=~/(\S)[\.-]*(\S)[\.-]*(\S)[\.-]*(\S)
+[\.-]*$/s){print "$1$2$3$4\n";}'

[download]
this simple command line takes hours to finish...does anyone have a better solution?

ok,i have a better solution,but why?... 

perl -e '$a="ATEH...GYS....I..CVNV...FGQ.....RTY.....F.YC.EY....G....D
+....TE....RL...R..E....V.IA..SVG.E.L-.-.---..-----...................
+...........................................................VPE.p-RTP.
+Y.A..M.S..V.TPA.TK---------.......-........---TS........IYGY.GT.R.P..
+......VP.......D...LQCVSISNWSMAR.......................KI..GE.Y...L..
+LE...-....--..-.....-..--........--...R..GF.P....V..Y................
+.....................................................................
+..............-...-..................................................
+....-.--....---EARV.D.P.L.TRL..V....IDR..RIT.T.............F.........
+..GW.............CS........V.N.......RY..--.----.......-....-.--.....
+.....................................................-...............
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+.....................................................................
+................-.-.---DW.RH..Q.G...R....S..........ST...C.....D.....
+IEV..D....CD.V.S...DL.V...A..V....P..D..DN.SW.-.......--..-P.L..YRC..
+L.S.F........DI.EC.....M..S..A.D......GG...---FPCAEKP...D.DIV........
+.I.QI..S.CV.CY.ET...G--.----..-Ggsadgaggvgvnggatpaptqshh.............
+.....................................................................
+........................gngesggipyypqaatagvgaqppVFG....R..SG..L......
+.H.....L......F.TI..GT.CDPVG--.....---..-.-...-..-.-----.............
+...---.----...........................EADV..Y..EF--.P....SEY.EL.LLGFM
+L.FFQRY.A..PSFMTGYNI.N...S..FDLKYILTR..L.E......Y..............L-.-.-
+..-..-..--...Y..K........................L.DV.QR.F..C.KVPV..AQGG....R
+FFLHSPT---..-...-LYrRH.Q.....D..RAS.FaaaA.A.NA..P..T.K...............
+V.....Y........IS..G..CV.VVD.MY.PVCM....A....KT.--......N...SP.N.YK.L
+N";if($a=~/.*(\w)[\.-]*(\w)[\.-]*(\w)[\.-]*(\
+w)[\.-]*/s){print "$1$2$3$4\n";}'

[download]

In reply to why this regular expression is so slow? by fnever

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