Bioinformatics FAQ

There are a large number of bioinformatics programs available to CBRG account holders via this web site. These examples (Frequently Asked Questions) are used to illustrate the use of these tools in answering typical queries posed by researchers.

The major web-based tools from the CBRG are listed, here.

Basic sequence manipulation

• Can I prepare a sequence figure for publication?
• How do I retrieve a sequence from the database?
• How do I translate a nucleotide sequence?
• What is the molecular weight/codon frequency of my protein?
• What is the GC content of my sequence?
• How do I reverse complement a sequence?

BLAST

• How do I search for short sequences (oligos) using BLAST?
• How do I run a BLAST search at the CBRG?

Alignments

• How can I create a global alignment of two sequences?
• How do I add colour to an alignment?
• Can I improve the appearance of an alignment?
• How can I create a multiple sequence alignment?
• How can I create a local alignment of two sequences?

Primer design

• How do I design PCR primers and hybridization oligonucleotides?

Proteins

• How can I search for transmembrane domains?
• How do I search for a defined pattern within a protein sequence?
• How do I search for any known motifs within a protein sequence?

Restriction analysis

• How do I look up information about an enzyme?
• Can I create a restriction site without altering translation?
• Can I destroy a restriction site without altering translation?
• Which enzymes cut my sequence?
• What fragments sizes are produced using this enzyme?
• Which enzymes do not cut my sequence?
• Which enzymes cut to leave a particular overhang?

Transcription factor binding sites

• What is the best way to search for transcription factor binding sites?
• Is there a database of transcription factor binding sites?

Sequence File Formats

• How do I convert between different sequence file formats

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