FAAz Help
  1. What's FAAz?
  2. What do it do?
  3. How to use?
  4. Examples
  5. Glossário
  6. About FAAz
FAAz - Fragment Assembly Analyzer.
Fragment Assembler Analyzer is a tool that compares consensus sequences resulting of PHRAP and CAP3 programs.
The goal is to allow a better view of each assembly. The idea came from the desire to automatically detect regions in both consensus sequences where a possibly assembler mistake occurred.
That is made through graphical outputs and quantitative results.

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Em linhas gerais, o FAAz procede da seguinte maneira:
- Roda o Blast 2 Sequence para cada par de consenso (phrap[i], cap3[j])
- Captura as saídas (hits) geradas tais que:
   + comprimento do hit seja maior ou igual ao valor do parâmetro <Minimum size of the region>; e
   + a razão comprimento do hit:comprimento do maior contig seja maior ou igual ao valor do parâmetro <Minimum value of region/contig>.
- Feito isso, consideramos "região" estes hits que restaram e "sub-região" a intersecção entre elas


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Esta é a tela inicial do FAAz



Funcionalidades:
1. Submissão da entrada, passando os arquivos e parâmetros.
2. Obtenção dos resultados, passando o ID.

Input files
* Archive of phrap '.ace':  File ACE from phrap program
* Archive of CAP3 '.ace':  File ACE from CAP3 program

Parameters
* The minimum size of the region: that number specifies the minimum size to a hit between the consensus sequences, one-to-one, contents in the ace´ files.
* Value to be added to Average Coverage: Especifies a free degree sobre the coverage.
* Minimum size of the overlap: Especifies the minimum size of the overlap to that it to be acepted.
* Minimum percentual size of region/contig: Espeficies the minimum value of the razao in percentual between region and contig.

Use case 1: Submit the entry

  1. Preencha os campos dos parâmetros, selecione os arquivos ACE´s e submeta-os.
  2. Será apresentada uma tela como esta:


  3. Será enviado um email para o usuário logado com o ID (este exibido na tela) quando o processo tiver sido finalizado.
  4. Com esse ID em mãos, você pode utilizar o Use Case 2.

Use Case 2: View results

  1. Submit the ID.
  2. Será exibida a tela de opções de views:


    3. OUTPUTS:

    1. Graphic of CAP to PHRAP / PHRAP to CAP
      Show graphic with subregions from CAP´s consensus to PHRAP´s consensus (or vice-versa)

      2. Include switches to view zoom and selected regions.

    2. PHRAP/CAP Coverage
      Show:
      • Similar regions between CAP3 and Phrap consensus sequence that was detected, labeled with the same number and separated at output with the correspondent label.

        • #############################################################
        #     ######### ##     ## ######### ######### #########     #
        #     ##     ## ##     ## ##     ## ##     ## ##     ##     #
        #     ##     ## ######### ######### ##     ## ##     ##     #
        #     ######### ##     ## #####     ######### #########     #
        #     ##        ##     ## ##  ###   ##     ## ##            #
        #     ##        ##     ## ##    ### ##     ## ##            #
        #############################################################

        or

        #############################################################
        #          ######### ######### ######### #########          #
        #          ##        ##     ## ##     ##        ##          #
        #          ##        ##     ## ##     ##        ##          #
        #          ##        ######### ######### #########          #
        #          ##        ##     ## ##               ##          #
        #          ######### ##     ## ##        #########          #
        #############################################################

      • In addition the label of each region you can see the initial and final positions of each similar region with length grater than 1500bp at consensus sequence (Phrap or Cap3), besides the sequence of bases.

      • After this, the reads that cover that region (even partially) are listed. Some additional information is supplied: the bases of the read that matches whit bases in the region are showed in uppercase (flagged with orange in this example). The initial and final positions of this occurrence in the read are informed as well the position where the first base of the read matches with consensus sequence.

      • The total number of reads that covers that region is found subsequently.

      • Next, the coverage of each part of region is listed (note that the same region can have different coverage), as well the names of reads participants. The sub-regions with different coverage are delimited with the first position relative to the consensus sequence.

      • This part is a little different at CAP3 list. The blast alignment can use the reverse of consensus sequence of CAP3, so, is not easy find the correspondent position at phrap consensus. To avoid this problem, we show the correspondent position besides the coverage.

      • The average coverage value

      • All sub-regions with coverage above the average plus 2 are reported.

      • The number of reads by region is showed.



    3. PHRAP / CAP not coverage

      4. Identifica as regiões do consenso gerado por um montador que não teve similaridade significante com nenhum consenso gerado pelo outro e aquelas que tiveram equivalência é mostrada a correspondência, ou seja, com qual contig existe similaridade.


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    O FAAz é um produto idealizado e desenvolvido no Biolab, tendo sua origem num projeto da disciplina Técnicas e Algoritmos Avançados de Computação no 2o. semestre do ano de 2002, ministrada pela professora Katia Guimarães. Team: Erico Souza Francisco Nascimento Jeane Bezerra Coordenate: Katia Guimarães

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