PDA v. 2: We have released a new version of PDA with much more functionality and ease of use. We encourage you to use this new version in http://pda.uab.es/pda2/.

 

PDA Home Page

News: PDA v.2 NOW AVAILABLE AT http://pda.uab.es/pda2/.                  PDA has successfully been used to create a database of nucleotide polymorphism in the Drosophila genus.


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PDA Help

Example

Download Source Code

Bugs in Older Versions

Input:

 

You can either:

1) Retrieve sequences from a database

Choose a database:                    Genbank / EMBL-Bank                  DPDB (only Drosophila genus)           

a) Enter a list of ORGANISMS and/or GENES:
         (e.g. Drosophila buzzatii or Actn) (a new line for each organism/gene)

ORGANISMS:    

GENES:            

     ... or ...

b) Enter a list of ACCESSION NUMBERS:
         (e.g. AY219224 if database is Genbank, or DPseq000526 if database is DPDB) (each in a new line)

     ... or ...

2) Introduce the sequences manually

a) Enter a list of SEQUENCES  (Fasta* and Genbank formats are allowed for unaligned sequences; alignments must be suplied in Fasta* format):

Enter or Paste a set of Sequences in any supported format :

Upload a file:

* Please, use the format >Organism|Gene in the header of each sequence if you want to specify this information in Fasta format. In Genbank format, end each record with // in a new line.
 

 

ONLY IF SEQUENCES FORMAT IS FASTA
 

 
  Codon start:  Assign all sequences to: , or change the values below*:   Alignment:  
    Align sequences
Do not align sequences (only if input sequences are already aligned)
 
 
* If you uploaded a file with the sequences, please write a line foreach sequence with its codon start as follows:
   Sequence 1 --> Codon start = 1
   Sequence 2 --> Codon start = 1
etc.
 
 

Main parameters:

 

       Analysis:

Synonymous and Non-Synonymous Substitutions
(only coding regions)
Linkage Disequilibrium
(only on each exon separately)
Sliding Window Length
(100 max):
Codon Bias
(only on coding regions)
 
Gene Annotations to study separately:

Alignments quality:

(CDS and exon will be selected automatically if the previous analyses are also selected)


(use Ctrl or Ctrl+Alt to select more than one item)

Minimum number of sequences per category:

Minimum ClustalW Score for pairwise comparisons (reduce or delete this parameter for very divergent sequences - HELP):

%

Minimum sequences length in the analyses:

Warning message if the proportion of excluded sites within an alignment (excluding end gaps) is greater than:

%

 

       Use the ESTIMATE OPTIMIZATION METHOD     [Help]

 

 

       Output database:

MySQL

Microsoft Access

 
If you want to be notified via e-mail as soon as the results are available in our server, please enter your e-mail address here:

Your E-MAIL: 
 
 

CLUSTALW parameters:

 
FAST PAIRWISE ALIGNMENT KTUP
(WORD SIZE)
WINDOW LENGTH SCORE TYPE TOPDIAG PAIRGAP
           
MULTIPLE ALIGNMENT GAP OPEN END GAPS GAP EXTENSION GAP DISTANCES

 

 

 





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