Blast

General Blast

We provide three blast databases which a gene or protein sequence of interest can be searched. There are two different type of blast searches that you can complete. A blastp search which compares amino acid against a protein sequence database, and a blastx search which compares a nucleotide sequence against a protein sequence database. For more information click on the program link.

There are three types of blast databases in which you can compare your sequence against the sequences in the INTERFEROME database. You can compare you sequence to either human IRG proteins, mouse IRG proteins or IRG proteins from all the species in our database. For more information click the database link.

When you enter a sequence into the search field you must enter it as a FASTA format, which begins with a single-line description, followed by lines of sequence data. For more information click the FASTA link above the search field box.


To search the database press search.

You can also search a subsequence of your input sequence, for example a domain or motif, by specifying a range of basepairs. i.e. for a 400bp region, specify a range from 100bp to 500bp, and only this range will be blasted against the sequences in the database.



The output file is similar to the one you obtain for normal NCBI blast.


Advanced Blast

You can also perform an advance BLAST analysis, in which you can select an E-value. This E-value describes the stringency of your blast. The Lower expectation value, the more stringent the database selects its results, leading to fewer chance matches being reported. There are six different expectation values you can specify, 10 which is the default, but you can have 0.0001 (highly stringent), 0.01, 1, 100, 1000 (very low stringency). More information can be obtained from the Expect link.



You can specify the Protein matrix that you will use, which assigns a score aligning any possible pair of residues. There five different matrices that you can choose from, BLOSUM62, BLOSUM80, BLOSUM45, PAM30 and PAM70. These are the same ones used in a normal blast search. For more information click the matrix link, which describes each matrix in more detail.


You can also select that the blast program will perform an ungapped alighment by ticking the box underneath the matrix select menu. There are different specifications for the graphical output of your results. The pull down link describes the type of alignments that you can have. These are pairwise alignment, master-slave with or without identities, flat master-slave with or without identities, Blast XML and Hit table.



You can also restricts the number of short descriptions of matching sequences reported, the maximum description limit is 500, and the lowest is 0 as seen in the descriptions pull down menu. For more information click the description link.



The alignments menu specify the number of high scoring segment pairs that are reported. The maximum that you can report is 500. If there are more database sequences than your alignment value, only the statistically significant results will be selected. For more information click the Alignment link.




You can also change the colour schema of the output data. There are seven different schemas to choose from.



Color schema 1:

• masked regions in lower case
• everything else in upper case

Color schema 2:

• masked regions in lower case, gray letters
• Unaligned regions in italic
• everything else in upper case


Color schema 3:

• No middle line.
• 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


Color schema 4:

• No middle line.
• Masked regions in lower case, gray letters
• Everything else in upper case
• Unaligned regions in italic
• Identity shown in blue color
• Similarity shown in brown color
• Mismatches shown in red color


Color schema 5:

• No middle line.
• Masked regions in lower case, gray letters
• Everything else in upper case
• Unaligned regions in italic
• Identity shown in red color
• Similarity shown in blue color
• Mismatches shown in black color


Color schema 6:

• No middle line.
• Masked regions in lower case, gray letters unless identity
• Everything else in upper case
• Unaligned regions in italic
• Identity shown in red bold color
• Similarity shown in blue color
• Mismatches shown in gray color


For more information click the colour schema link.

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