blast.uthsc.edu

BLAST Search

P450 Blast Server Documentation. Choose program to use and database to search:. Tribolium (red flour beetle). All public named insect P450s). All public invertebrate non-insect P450s). C elegans and C. briggsae. All named fungal P450s. Enter sequence below in FASTA. Or load it from disk. The query sequence is NOT filtered. For low complexity regions by default. Mask for lookup table only. Query Genetic Codes (blastx only). Mold Mitochondrial; . (4). Ciliate Nuclear; . (6). Alternative Yeast Nuclear (12).

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BLAST Search | blast.uthsc.edu Reviews

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P450 Blast Server Documentation. Choose program to use and database to search:. Tribolium (red flour beetle). All public named insect P450s). All public invertebrate non-insect P450s). C elegans and C. briggsae. All named fungal P450s. Enter sequence below in FASTA. Or load it from disk. The query sequence is NOT filtered. For low complexity regions by default. Mask for lookup table only. Query Genetic Codes (blastx only). Mold Mitochondrial; . (4). Ciliate Nuclear; . (6). Alternative Yeast Nuclear (12).

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1 program

2 blastp

3 blastx

4 database

5 human

6 mouse

7 cattle revised

8 arabidopsis

9 rice combined

10 chlamydomonas and volvox

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program,blastp,blastx,database,human,mouse,cattle revised,arabidopsis,rice combined,chlamydomonas and volvox,drosophila,anopheles,aedes aegypti,silkworm,pea aphid,nasonia wasp,honeybee,daphnia,all protist sequences,dictyostelium,paramecium tetrauralia

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BLAST Search | blast.uthsc.edu Reviews

https://blast.uthsc.edu

P450 Blast Server Documentation. Choose program to use and database to search:. Tribolium (red flour beetle). All public named insect P450s). All public invertebrate non-insect P450s). C elegans and C. briggsae. All named fungal P450s. Enter sequence below in FASTA. Or load it from disk. The query sequence is NOT filtered. For low complexity regions by default. Mask for lookup table only. Query Genetic Codes (blastx only). Mold Mitochondrial; . (4). Ciliate Nuclear; . (6). Alternative Yeast Nuclear (12).

INTERNAL PAGES

blast.uthsc.edu

1

FASTA format description

http://blast.uthsc.edu/docs/fasta.html

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (" ") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA. The nucleic acid codes supported are:. For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:. A alanine P proline B aspartat...

2

Matrix and Gap Costs

http://blast.uthsc.edu/docs/matrix_info.html

Query length Substitution matrix Gap costs - - - - - - - - - - - - - - - - - - - - -. 85 BLOSUM-62 (11,1). Altschul, S.F. (1991) "Amino acid substitution matrices from an information theoretic perspective." J. Mol. Biol. 219:555-565. [2] States, D.J., Gish, W. and Altschul, S.F. (1991) "Improved sensitivity of nucleic acid database searches using application-specific scoring matrices." Methods 3:66-70. [3].

3

Programs available for the BLAST search

http://blast.uthsc.edu/docs/blast_program.html

Programs available for the BLAST search. Family of programs includes:. Compares an amino acid query sequence against a protein sequence database. Compares a nucleotide query sequence against a nucleotide sequence database. Compares a nucleotide query sequence translated in all reading frames against a protein sequence database. Compares a protein query sequence against a nucleotide sequence database dynamically translated in all reading frames.

4

BLAST Color schema description

http://blast.uthsc.edu/docs/color_schema.html

BLAST Color schema description. Masked regions in lower case. Everything else in upper case. Masked regions in lower case, gray letters. Unaligned regions in italic. Everything else in upper case. Masked regions in lower case, gray letters unless identity. Everything else in upper case. Unaligned regions in italic. Identity shown in red color. Similarity shown in blue color. Mismatches shown in black color. Masked regions in lower case, gray letters. Everything else in upper case.

5

Out-of-frame notation

http://blast.uthsc.edu/docs/oof_notation.html

When protein aligned to the nucleotide there are 6 possibilities of match at any point. In OOF alignment - upper sequence is DNAP - 3-frame translated DNA. Lower sequence is protein. At any position next protein base may be aligned to 6 possible bases in DNAP:. TBO - traditional blast output). 0: 3 nucleotides missing - gap (TBO notation "-"). 1: 2 nucleotides missing - "frameshift -2" (TBO notation " "). 2: 1 nucletide missing - "frameshift -1" (TBO notation " "). OOF alignment with DNAP: DTRGGDTPQKSVFS...

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BLAST Search

P450 Blast Server Documentation. Choose program to use and database to search:. Tribolium (red flour beetle). All public named insect P450s). All public invertebrate non-insect P450s). C elegans and C. briggsae. All named fungal P450s. Enter sequence below in FASTA. Or load it from disk. The query sequence is NOT filtered. For low complexity regions by default. Mask for lookup table only. Query Genetic Codes (blastx only). Mold Mitochondrial; . (4). Ciliate Nuclear; . (6). Alternative Yeast Nuclear (12).

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