Current version: 2.0


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INPUT FROM DATABASE:

1) Choose a database:

Genbank / EMBL-Bank

DPDB (sequences of the Drosophila genus)

MamPol (sequences of the Mammalia class)

 

2) Enter a list of:

ORGANISMS and/or GENES:

ORGANISMS, TAXONOMY GROUPS OR ALIASES: (e.g. Drosophila melanogaster, Cetacea or cow) (a new line for each item)
GENES: (e.g. Actn) (a new line for each gene)

ACCESSION NUMBERS:

(e.g. AY219224 if database is Genbank, or DPseq000526 if database is DPDB, or MAMseq000526 if database is MamPol) (a new line for each accession number)

 

 

INPUT SEQUENCES MANUALLY:

Enter a list of SEQUENCES:


Upload a file:
  FORMATS SUPPORTED:

- Unaligned sequences: FASTA (use the format >Organism|Gene in each sequence header if you want to specify this information) or GENBANK (each record ends with // in a new line)

- Aligned sequences: FASTA (use the format >Organism|Gene in each sequence header if you want to specify this information)
 

 

 

ONLY IF SEQUENCES FORMAT IS FASTA
 

 
  Codon start:  Assign all sequences to: , or change the values below*:   I want PDA to:  
    Align my sequences
Do not align my 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:

1) Optional analyses:

Synonymous and Non-Synonymous Substitutions (in coding regions only)

Linkage Disequilibrium (in exons and introns only)
             Sliding Window Length (100 max):

Codon Bias (in coding regions only)
 
2) Regions to be studied separately (CDS, exon and intron will be selected automatically with the optional analyses): 3) Alignments quality:  

(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:

 

 


4) Other parameters:

Use the ESTIMATE OPTIMIZATION METHOD     [Help]

 You can enter a TITLE for this analysis:   

 

 

ALIGNMENT PARAMETERS:

Select an alignment program:
 
ClustalW Muscle T-Coffee

 

If ClustalW, you can change default parameters:

1) Fast Pairwise Alignment:

KTUP (WORD SIZE):
WINDOW LENGTH:
SCORE TYPE:
TOPDIAG:
PAIRGAP:

2) Multiple Alignement:

GAP OPEN
END GAPS
GAP EXTENSION
GAP DISTANCES

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UAB       DGM