Nucleotide and Protein Information

1. Nucleotide and Protein Search Engines
2. Nucleotide and Protein data files:
   • Nucleotide and protein sequences.
   • Expressed sequence tags of Plasmodial genes.
   • A chromosome probe list.
   • Restriction sites in Plasmodium falciparum.
   • Malaria strain information.
   • Malaria Antigen Information.

Nucleotide and Protein Search Engines

• SRS - To search for a sequence from our nucleotide and protein FTP files, using the Sequence Retrieval System software, by Thure Etzold.

• Codon Usage Database - Codon Usage Database compiled from CUTG (Codon Usage Tabulated from GenBank).

• Or use our own search engines for the nucleotide and protein FTP files (searches information from both before and after the last mailout) :-

Search sequence: xxx and yyy - returns all nucleotides sequences containing both xxx and yyy. Can use multiple 'and's.
Search sequence: xxx or yyy - returns all nucleotides sequences containing either xxx or yyy. Can use multiple 'or's.
Any attempt to use the 'or' operator with the 'and' operator will result in the 'or' being considered as part of the search sequence.
Sequences may be expressed in upper or lower case letters.

This search returns all proteins that contain the codon search sequence, for example: MSKVQKDSAK

Codon Search Sequence: xxx and yyy - returns all proteins sequences containing both xxx and yyy. Can use multiple 'and's.
Codon Search Sequence: xxx or yyy - returns all proteins sequences containing either xxx or yyy. Can use multiple 'or's.
Any attempt to use the 'or' operator with the 'and' operator will result in the 'or' being considered as part of the Codon Search Sequence.
Sequences may be expressed in upper or lower case letters.

Nucleotide and Protein data files:

• This directory lists files that were included in the last mailout.
  
  • Annotated Nucleotide sequences in EMBL format. Beware that this is a very large file occupying about 6.5 Mb at last count. A list of entries in this file can be obtained here.
  • Unannotated nucleotide sequences suitable for importation into PC programs
  • Annotated Protein Sequences in EMBL format
  • Unannotated protein sequences suitable for importation into PC programs
  • List of expressed sequence tags of Plasmodial genes These are included in annotnuc.dat but are separately listed here with BLAST search results for each EST.
  • Annotated Nucleotide sequences in GCG format. Note: this directory contains thousands of files and takes a while to list in your web browser.

    Malaria Genome Information

  • The chromosome probe list tells you about known chromosome markers for the 14 chromosomes of P. falciparum.
  • The list is cross-referenced to the database and the chromosome probe list so that you can identify a researcher who can supply you with an appropriate probe.

• Restriction sites in Plasmodium falciparum: This data was supplied by Leda Cummings of the Institute for Genomics Research (TIGR).
  In a search for improvement of our current YAC end rescue protocols I asked Herve Tettelin to generate a table containing all possible hexamers and their frequencies in P. falciparum genome, using our current 1,300.000 sequence reads for chromosome 2.

• Malaria strain information: The WHO funds a malaria strain bank that is maintained at the Institute of Cell and Animal Biology, University of Edinburgh by Dr David Walliker. Listed here are the various isolates and cloned lines of malaria that are available by contacting David. I have added a table listing the origin of commonly used P. falciparum isolates.
  • P. falciparum isolates
  • P.falciparum cloned lines
  • Mouse malaria strains
  • Origin of P.falciparum lab isolates.

• Malaria antigen information:
  • Bibliographies
  • Antigen alignments

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