[Bioperl-l] creating a simplealign object from strings

[Remo Sanges]

On Oct 20, 2004, at 4:38 PM, luisa pugliese wrote:

> Dear all,
>     I am working with a huge protein alignment that comes from a web  
> page
> and I would like to import it into bioperl. In order to do this I  
> created a
> hash with seqnames as keys and sequences, including gaps, as values.  
> Then I
> used LocatableSeq in order to create sequence objects that can be then
> imported into a simplealign object with the function add_seq.
> Using LocatableSeq I got the following error:
> ----------------------------
> MSG: Attempting to set the sequence to
> [----------DPQMWDFDDLNFTG-MP-PADE-DYSPCMLET-ETLNKYVV---II---AYA--LVF-- 
> L--LSL
> LGNSL-----VM----L----VILY-----SRV-----GR-----SV-TD-----V--YL-LN- 
> LALADLLFAL--
> ---TLPIWAASKV-----NG------WIF--GTF-----LC-KVVSL----L----K----E----- 
> VN---FY--
> -SG-I-----LL-----LACISV--D-R--YL-----AIVH---ATR---T-----L----TQ---K--- 
> RH----
> L-----VK-FV-----CLG-----CWGLSMNLSL-----PFFLFRQ----AY-----HPNNSSP-- 
> VCYEVLG---
> --NDTAKWRMVL-----RI--LPHT--FGFIVPLFVMLFCYGF- 
> TLRTLFKAHM-----------------GQ---
> -KHR-----A---M-RVIFAVV-LIFLLC---WLP---- 
> YNLVLLADTLMRTQV7TCERRNNIGRALDATEILGFL
> ---H---SC-----L--NP----IIYA-----FIGQ---N-----FRH----GF-----L-----K-- 
> ILAMHGLV
> SKEFLA--RHRVTS-----------------------------] which does not look  
> healthy

Probably you have a problem in parsing your web page...

If you check the lines of your sequence you can see a number in this:
-KHR-----A---M-RVIFAVV-LIFLLC---WLP---- 
YNLVLLADTLMRTQV7TCERRNNIGRALDATEILGFL

This is why your sequence 'does not look healthy' to bioperl

Trying to correct this should solve your problem

HTH

Remo