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After read cleaning this pipeline will call Abyss for denovo assembly in contigs. The resulting contigs can be further assembled with CAP3. The contigs are then blasted against a provided multi-fasta file and/or ncbi databases. If a blastx on nr is chosen the result can be used to annotate the best hits with blast2go.

Author(s)

MBB dev


Version

1


Subsections

Pipeline - Blast - Assembler


Tags

De novo


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Bl2seq

Blast

 

The program bl2seq is designed to compare two input FASTA sequences directly bypassing the formatdb step. This allows users to quickly assess the similarities between two input sequences. The program is capable of performing six types of blast searches: blastn, blastp, blastx, tblastn, tblastx, and megabalst in place of blastn.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

1


Subsections

Blast


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Used in order to build a database on a given sequence file and perform a Blast on it. Useful to realize reciprocal Blast. The proposed version of formatDB and Blast are those including MPI compatibility. Then each execution use 8 cores to reduce execution time.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman ... [wrapper : MBB development team]


Version

1


Subsections

Blast


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BLAST2

Blast

 

The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while enhancing their sensitivity to weak similarities. A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original. In addition, a method is introduced for automatically combining statistically significant alignments produced by BLAST into a position-specific score matrix, and searching the database using this matrix. The resulting Position-Specific Iterated BLAST (PSI-BLAST) program runs at approximately the same speed per iteration as gapped BLAST, but in many cases is much more sensitive to weak but biologically relevant sequence similarities. PSI-BLAST is used to uncover several new and interesting members of the BRCT superfamily.

Author(s)

Altschul, Madden, Schaeffer, Zhang, Miller, Lipman


Version

2


Subsections

Blast


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BLASTClust is a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. The program begins with pairwise matches and places a sequence in a cluster if the sequence matches at least one sequence already in the cluster. In the case of proteins, the blastp algorithm is used to compute the pairwise matches; in the case of nucleotide sequences, the Megablast algorithm is used.

Author(s)

Ilya Dondoshansky, Yuri Wolf


Version

2.2.21


Subsections

Blast


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