AB-BLAST 与 WU-BLAST的不同点

Apart from bug fixes, the most outward differences in usage and appearance of AB-BLAST and WU-BLAST include:

• The default scoring system for AB-BLASTN is match/mismatch scores M=+1 N=−3 with gap penalties Q=7 R=2; whereas WU-BLASTN uses M=+5 N=−4 with gap penalties Q=10 R=10 by default.
• In all search modes, the default value for the gapped alignment drop-off score gapX is ≈50% higher for AB-BLAST, which will tend to make the AB-BLAST search programs slightly more sensitive and just slightly slower.
• AB-BLAST supports an expanded amino acid alphabet, compared to the amino acid alphabet used by WU-BLAST. Programs in the WU-BLAST package are consequently unable to search or modify protein sequence databases that were created or modified by AB-xdformat. Once a protein sequence database created with WU-xdformat has been modified by AB-xdformat, it can no longer be searched or modified by any of the WU-BLAST programs. Databases created by WU-xdformat can be searched and modified by the AB-BLAST programs. At least for the time being, the AB-BLAST search programs can also search virtual databases that are a combination of databases created with WU-xdformat and AB-xdformat.
  No difference currently exists between the nucleotide alphabets used by AB-BLAST and WU-BLAST or the ability of programs in either package to search/modify nucleotide sequence databases created/modified by programs in the other package.
• The bundled BLOSUM30 and BLOSUM35 scoring matrices have been re-scaled to provide better precision.
• The bundled amino acid scoring matrices — and the matrices output by the pam program — now contain a J row and a J column. These matrices are incompatible with WU-BLAST, which does not support the letter J and will report a FATAL error when reading the files. The AB-BLAST amino acid scoring matrices are slightly different from the matrices distributed by the NCBI, which also indicate scores for the letter J, but at the time of this writing the NCBI matrices are cross-compatible with AB-BLAST.
• AB-BLAST supports the amino acid letter code O (“oh”) normally used to represent Pyrrolysine (Pyl), whereas WU-BLAST does not. The letter O may appear in query sequences, database sequences, scoring matrix files and with command line parameters such as the altscore option, but the scoring matrices bundled with AB-BLAST do not actually utilize this letter. The default score for aligning any other letter with O is the same score as for aligning with X, whereas the O self-alignment score defaults to zero (0).
• The AB-BLAST 3.0 search programs support a new compat2.0 option to obtain roughly equivalent parameter settings to those used by WU-BLAST 2.0.
• The analog to wu-blastall is named ab-blastall.
• The analog to wu-formatdb is named ab-formatdb.
• AB-BLAST programs preferentially use settings of the new environment variables ABBLASTMAT, ABBLASTDB and ABBLASTFILTER. See the section on Environment Variables for important details. When upgrading from WU-BLAST to AB-BLAST, due to the support for the letter J in AB-BLAST, it is important to ensure that the AB-BLAST search programs use the bundled scoring matrices rather than the old matrices that were distributed with WU-BLAST, because of the latter matrices’ lack of support for the letter J.
• The maximum allowable value for the dbslice parameter has been increased.
• The sp2fasta program parses input more reliably.
• Each release of AB-BLAST is generally distributed in 3 “Editions” — Personal, Standard and Enterprise — which differ from each other in the degree of parallelism they support, whereas WU-BLAST was distributed in a single version.
• The first few lines of output, including the program declaration line and copyright notice, are different. See Citing BLAST for examples of the program declaration line from AB-BLAST.
• Programs in the AB-BLAST package that use the UNIX standard getopt() function to parse the command line will now uniformly across all computing platforms produce “POSIXLY_CORRECT” behavior. (N.B. The BLAST search programs do not use getopt(), but most other programs in the package, including xdformat and xdget, do). This means some command lines that are acceptable to WU-BLAST on some computing platforms (usually Linux) may be rejected by AB-BLAST and need to be restructured. This can happen if all parameters and flags are not specified before (to the left of) the required command line arguments.
• Better thread management under energy conservation conditions.
• Better memory management under Mac OS X.