[Bioperl-l] hmm alignment

[stephan.rosecker at ish.de]

hi list,

i'm looking for a way to get the alignment from an hmmpfam output.
I like to show the aligmnet e.g on the commandline in the same
format as hmmpfam, is there an easyer way to do this, or only possible
in manual operation with:
$hsp->query_string;
$hsp->hit_string; 
... some string operationes
(HMMERHSP get_aln() is deprecated ...)


This is what i want...


                   *->GIeEkIkaIEeEiarTqKNKATEyHLGlLKaKLAkLReQLlEpskgg
                       I+EkI aIE E+arTqKNKAT  HLGlLKa  AkLR +L   s +g
  128U_DROME     4    -ILEKISAIESEMARTQKNKATSAHLGLLKANVAKLRRELI--SPKG 47   

                   gGGG...kGFeVeKSGdarvaLIGfPSVGKStLLakLTntkSEvAdYaFT
                   gGGG+++ GFeV+K Gdarv ++GfPSVGKStLL+ L +  SEvA+Y+FT
  128U_DROME    48 GGGGtgeAGFEVAKTGDARVGFVGFPSVGKSTLLSNLAGVYSEVAAYEFT 97   

                   TLTcvPGvLeYqgakIQllDlPGIIeGAssGKGRGrqVlAvarsADLvLm
                   TLT vPG ++Y+gakIQllDlPGIIeGA  GKGRGrqV+Avar+  L+ m
  128U_DROME    98 TLTTVPGCIKYKGAKIQLLDLPGIIEGAKDGKGRGRQVIAVARTCNLIFM 147  

                   vLDatkleehrdvLekELEnVGIRLnkrkGPniyfKkKetGGvsvngTgp
                   vLD  k+ +h  +Le ELE  GIRLnk++ Pniy+K K  GG++ n+ +p
  128U_DROME   148 VLDCLKPLGHKKLLEHELEGFGIRLNKKP-PNIYYKRKDKGGINLNSMVP 196  

                   PLThidEdtvrrILheYRIhNAeVliReDqvTlDdFIDVVnegNRvYipc
                      ++d d+v++IL+eY+IhNA++  R D +T Dd IDV+ egNR Yipc
  128U_DROME   197 -QSELDTDLVKTILSEYKIHNADITLRYD-ATSDDLIDVI-EGNRIYIPC 243  

                   LyVyNKIDlvgieevdrlarkrlEiGpntIVvScnmglnLdelaerlwek
                   +y +NKID+++iee+d + +      p  + +S+    n d+l+e +we 
  128U_DROME   244 IYLLNKIDQISIEELDVIYKI-----PHCVPISAHHHWNFDDLLELMWEY 288  

                   LglvRVYtKkqGkePDFDPLvepLilRrGsT.VeDvChhiHrDLvrrFKY
                   L l R+YtK++G+ PD+     p +l +  T++eD+C+++Hr  +++FKY
  128U_DROME   289 LRLQRIYTKPKGQLPDYN---SPVVLHNERTsIEDFCNKLHRSIAKEFKY 335  

                   AlVWGkSaKhppQrVGleHvleDeDvvqivvK<-*
                   AlVWG+S+Kh pQ+VG+eHvl DeDvvqiv+K   
  128U_DROME   336 ALVWGSSVKHQPQKVGIEHVLNDEDVVQIVKK    367