I have recently installed blast 2.2.24+ and I was looking for the bl2seq tool, but I didnt find it. After some research I found that bl2seq is only found in the legacy blast package. So my question is how can I run blast 2 sequences in the blast+ package. Thank you so much
As shown in the diagram in "4.1 Functionality offered by BLAST+ applications" the functionality of the 'bl2seq' tool has been folded into the main BLAST programs. So you can now do something like:
blastp -query querySeqs.tfa -subject targetSeqs.tfa
To perform a pairwise BLAST alignment of a set of sequences.
Of course this will use the BLAST algorithm to perform the alignment. Since BLAST is an approximate local sequence alignment method, depending on your requirements, you may want to look at alternative methods. For example:
Needleman-Wunsch global alignment. The original sequence alignment method, Needleman-Wunsch produces optimal global (i.e. end-to-end on both query and subject) alignments. This is implemented in a number of tools including: the 'needle' and 'needleall' programs in EMBOSS and the GGSEARCH program in the FASTA suite. A common modification of this method is the Myers and Miller algorithm which reduces the memory requirements, this used in EMBOSS 'stretcher' and ClustalW 2.
Smith-Waterman local alignment. Produces optimal local alignments, example implementations include: the 'water' program in EMBOSS and the SSEARCH program in the FASTA suite. Again modifications of the original method are commonly used, such as Waterman-Eggert with is implemented in EMBOSS 'matcher' and lalign in the FASTA suite.
The commonly used sequence similarity search methods FASTA and BLAST are approximations based on the Smith-Waterman local alignment method. These sacrifice some sensitivity in order to improve speed. This trade off is important when dealing with large databases, but for smaller sets of alignments and small databases using the more rigorous methods is a realistic option.
If you want to experiment with some alternative pairwise alignment methods EMBL-EBI's collection of pairwise alignment services and sequence similarity search services may provide a reasonable place to start, although being on-line tools there are some limitations not present in the command-line versions.
Type "blastn -help". You will find
*** BLAST-2-Sequences options -subject <File_In> Subject sequence(s) to search * Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask -subject_loc <String> Location on the subject sequence in 1-based offsets (Format: start-stop) * Incompatible with: db, gilist, seqidlist, negative_gilist, db_soft_mask, db_hard_mask, remote
Use one of these instead of "-db".