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Sequence alignment with blastall

Blastall is one of the most commonly used blast programs, its function is very powerful, there are many parameters under it, but generally used parameters such as:-p,-I,-d,-o,-e and so on.

-p: name of the program executed

-d: name of the database searched

-I: the sequence file name to be queried (Query File)

-e: (mathematics) expected value (Expectation value), E value is a statistical threshold, the default value is 10, which means that the matching result caused by random chance in the comparison result is not greater than 10, the smaller the E value, the more reliable the result.

-o: query result output file name

-m: compare the result display format option, the default value is 0, that is, pairwise format. In addition, different formats such as 1x 6 can be selected according to different needs.

-I: display the gi number [Tmax F] in the description line, the default value F

-v: the maximum number of single-line descriptions (one-line description), with a default value of 500

-b: the maximum number of alignment results displayed, with a default of 250

-F: filter the low complexity region (low complexity regions, LCR) of the sequence to be queried [T], the default value is T. DUST program is used for blastn, and SEG program is used for other comparisons.

The so-called "low complexity region" refers to the excessive expression of some or some residues, short period repetition and so on. For the genome sequence of higher mammals, the repetitive elements can be masked by the RepeatMask program. In the output result, nucleic acid in LCR region is replaced by "N" and protein sequence is replaced by "X".

-a: the number of processors used to run BLAST programs. The default is 1.

-S: the strand used when searching the database, valid only for blastn, blastx, and tblastx; 1 for top,2, bottom,3 for both;, default value 3

-T: produces the output in HTML format [T _ Pot F], default value F

-n: use MegaBlast to search for [Tmax F], the default value is F

-G: turn on a penalty score for gap (0 means to use the default setting). The default is 0.

-E: extend the penalty score of a gap (0 means to use the default setting). The default is 0.

-Q: penalty score for a nucleic acid base mismatch (mismatch) (valid for blastn only), default value-3

-r: a score for correct matching of nucleic acid bases (match) (valid for blastn only), default value 1

-M: the scoring matrix used, the default BLOSUM62

1.1.1. Parameter description

Basic parameters, comparison optimization parameters, result output parameters, control input parameters

Table: parameter description of the blastall command

Parameter description default value Note-the program character [String] blastnblastpblastx used by p

Tblastn

Tblastx

-d database filename [File In] nr-i search sequence filename [File In] stdin-e expected number [Real] 10.0Lill m controls integers [Integer] 00 = pairwise,1 = query-anchored showing identities,2 = query-anchored no identities that compare the style of the result to 11

3 = flat query-anchored, show identities

4 = flat query-anchored, no identities

5 = query-anchored no identities and blunt ends

6 = flat query-anchored, no identities and blunt ends

7 = XML Blast output

8 = tabular

9 tabular with comment lines

10 ASN, text

11 ASN, binary

-O compare the file name stored in the result [File Out] stdout-F filter query sequence [String] TDUST with blastn, SEG with others-G open gap score [Integer]-1While E extension gap score [Integer]-1-XX dropoff value for gapped alignment (in bits) [Integer] 0blastn 30, megablast 20, tblastx 0 All others 15muri display gi number Show GI's in matches [T / F] Fmurq nucleic acid mismatch penalty score [Integer]-3blastn only-r nucleic acid matching score [Integer] 1blastn only-vNumber of database sequences to show one-line descriptions for (V) [Integer] 500-bNumber of database sequence to show alignments for (B) [Integer] 250-fThreshold for extending [Integer] 0blastp 11, blastn 0, blastx 12, tblastn 13, tblastx 13 Megablast 0-gPerform gapped CPU [T / F] Tnot available with tblastx-Q specifies the genetic code used by the query sequence [Integer] 1 genetic code used by the specified data [Integer] 1for tblast [nx] only-a number of CPU [Integer] 1-OSeqAlign file [File Out] optional-matrix [String] BLOSUM62-WWord size [Integer] 0blastn 11, megablast 28 used by the comparison of JBelieve the query sequences [T / F] Fmurm Effective length of all others 3murz database Effective length of the database [Real] 0use zero for the real size-KNumber of best hits from a region to keepInteger] 0off by default, if used a value of 100is recommended-P0 for multiple hit, 1 for single Hitt [Integer] 0does not apply to blastn-YEffective length of the search space [Real] 0use zero for the real size-SQuery strands to search against database [Integer] 3for blast [nx], and tblastx, 3 is both, 1 is top 2 is bottom-T saves the result in HTML format [T _ bot F] Fmurl through the list of gi numbers Limit the search scope [String] Optional-UUse lower case filtering of FASTA sequence [T / F] Optional-yX dropoff value for ungapped extensions in bits [Real] 0.00.0 invokes default behavior blastn 20, megablast 10, all others 7-ZX dropoff value for final gapped alignment in bits [Integer] 0blastn/megablast 50, tblastx 0, all others 25-RPSI-TBLASTN checkpoint file [File In] Optional-nMegaBlast search [T / F] F-LLocation on query sequence [string] Optional-AMultiple Hits window size [Integer] 0default if zero (blastn/megablast 0 All others 40)-wFrame shift Penalty [Integer] 0OOF algorithm for blastx-tLength of the largest intron allowed in a translated nucleotide sequence when linking multiple distinct alignments [Integer] 00 invokes default behavior A negative value disables linking.-BNumber of concatenated query [Integer] 0for blastn and tblastn-VForce use of the legacy BLAST en Gine [T / F] FOptional-CUse composition-based statistics for tblastn [String] DD or d: default (equivalent to F) 0 or For f: no composition-based statistics 1 or T or t: Composition-based statistics as in NAR 2994-3005, 2001

2: Composition-based score adjustment as in Bioinformatics 21R 902-911

2005, conditioned on sequence properties

3: Composition-based score adjustment as in Bioinformatics 21VR 902-911

2005, unconditionally

For programs other than tblastn, must either be absent or be D, For 0.

-sCompute locally optimal Smith-Waterman signals [T / F] FThis option is only available for gapped tblastn.1.1.2. Instructions and examples

Instructions for program use

Program name search sequence database Note blastn nucleic acid search nucleic acid sequence search nucleic acid database blastp protein protein search protein (amino acid) sequence search protein database for higher scores, not suitable for distant relationships, blastx nucleic acid proteins search all translation results of the six theoretical frameworks of nucleic acid double-stranded sequences Analytical translation search sequence for new sequences and ESTs tblastn protein nucleic acid for search for proteins and nucleic acids in the database tblastx nucleic acid alignment command example # build library makeblastdb-in HSP20_NCBI_pep.fasta-dbtype prot-title HSP20_NCBI_pep.fasta # protein sequence # blastp alignment blastall-I Arabidopsis_thaliana.TAIR10.pep.all.fa-d nucleic acid _ pep.fasta-p blastp-e 1e-10-b 1-v 1-m 8-o ncbi_hsp.out so far I believe that you have a deeper understanding of "what are the parameters of blastall?" you might as well do it in practice. Here is the website, more related content can enter the relevant channels to inquire, follow us, continue to learn!

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