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I have 6 genes of Candida albicans yeast namely orf19.723, orf19.5908, orf19.610, orf19.2119, orf19.4998 and orf19.4056. And I have found the corresponding ortholog genes from Broad Institute website of other 16 species of yeast. So I have all gene names. Now how would I specifically download these genes and from where can I do this, preferably in an automated manner?

Also is there any standard naming convention? Because the ORF names given have other names too like BCR1, EFG1 and NDT80.

The list of gene names I have :

The orthologs of C. Albicans with S. cerevisiae
orf19.2119  YHR124W 
orf19.4998  YBR033W YKL034W 
orf19.5908  YBR083W 
orf19.610   YMR016C YKL043W 
orf19.723   NONE
orf19.4056  YMR136W 

The orthologs of C. Albicans with S. paradoxus
orf19.2119  spar33-g1.1 
orf19.4998  spar197-g23.1   spar324-g3.1    
orf19.5908  spar200-g4.1    
orf19.610   spar184-g1.1    spar324-g10.1   
orf19.723   NONE
orf19.4056  spar165-g2.1

The orthologs of C. Albicans with S. mikatae
orf19.2119  NONE
orf19.4998  smik146-g12.1   smik109-g17.1   
orf19.5908  smik83-g2.1 
orf19.610   smik571-g2.1    smik109-g10.1   
orf19.723   NONE
orf19.4056  smik1535-g1.1   

The orthologs of C. Albicans with S. bayanus
orf19.2119  sbayc514-g9.1   
orf19.4998  sbayc611-g22.1  sbayc652-g20.1  
orf19.5908  sbayc678-g131.1 
orf19.610   sbayc638-g23.1  sbayc652-g27.1  
orf19.723   NONE
orf19.4056  sbayc657-g41.1

The orthologs of C. Albicans with S. castellii
orf19.2119  Scas697.24  
orf19.4998  Scas625.4   
orf19.5908  Scas718.27  Scas635.12  
orf19.610   Scas106.1   Scas709.52  Scas625.8   
orf19.723   NONE
orf19.4056  Scas680.22d 

The orthologs of C. Albicans with C. glabrata
orf19.2119  CAGL0L13090g    
orf19.4998  CAGL0L01947g    
orf19.5908  CAGL0M01716g    CAGL0F04081g    
orf19.610   CAGL0M07634g    CAGL0L01771g    
orf19.723   NONE
orf19.4056  CAGL0I00902g    CAGL0L06776g    

The orthologs of C. Albicans with S. kluyveri
orf19.2119  SAKL0E11330g    
orf19.4998  SAKL0A09812g    
orf19.5908  SAKL0B06578g    
orf19.610   SAKL0D13442g    
orf19.723   SAKL0A03476g    
orf19.4056  SAKL0E04862g    

The orthologs of C. Albicans with K. lactis
orf19.2119  KLLA0F24420g    
orf19.4998  KLLA0F25674g    
orf19.5908  KLLA0E12507g    
orf19.610   KLLA0F04840g    
orf19.723   NONE
orf19.4056  KLLA0F17116g    

The orthologs of C. Albicans with A. gossypii
orf19.2119  AGR347W 
orf19.4998  AFR275W 
orf19.5908  AER177W 
orf19.610   ABR055C 
orf19.723   NONE
orf19.4056  ADR249W 

The orthologs of C. Albicans with K. waltii
orf19.2119  Kwal33.14699    
orf19.4998  Kwal26.8099 
orf19.5908  Kwal27.12423    
orf19.610   Kwal26.8176 
orf19.723   NONE
orf19.4056  Kwal47.17849    

The orthologs of C. Albicans with C. tropicalis
orf19.2119  CTRG01097.3 
orf19.4998  CTRG03636.3 
orf19.5908  CTRG02294.3 
orf19.610   NONE
orf19.723   CTRG00608.3 
orf19.4056  CTRG04523.3 

The orthologs of C. Albicans with L. elongosporus
orf19.2119  LELG01178   
orf19.4998  NONE
orf19.5908  LELG02666   
orf19.610   LELG05390   
orf19.723   LELG03123   
orf19.4056  LELG01761   

The orthologs of C. Albicans with C. parapsilosis
orf19.2119  CPAG04608   
orf19.4998  NONE
orf19.5908  CPAG01691   
orf19.610   CPAG00178   
orf19.723   CPAG00564   
orf19.4056  CPAG05034   

The orthologs of C. Albicans with D. hansenii
orf19.2119  DEHA2A07282g    
orf19.4998  NONE
orf19.5908  DEHA2G13794g    
orf19.610   DEHA2E10978g    
orf19.723   DEHA2E05984g    
orf19.4056  DEHA2E07172g    DEHA2F25916g    

The orthologs of C. Albicans with C. guilliermondii
orf19.2119  PGUG02096.1 
orf19.4998  NONE
orf19.5908  PGUG04378.1 
orf19.610   PGUG03651.1 
orf19.723   PGUG05571.1 
orf19.4056  PGUG05533.1 

The orthologs of C. Albicans with C. lusitaniae
orf19.2119  CLUG00404   
orf19.4998  NONE
orf19.5908  CLUG04694   
orf19.610   CLUG02047   
orf19.723   CLUG00627   
orf19.4056  CLUG05535
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  • 2
    $\begingroup$ You could check out biopython if you are comfortable with Python programming $\endgroup$ – Luigi Dec 24 '14 at 6:51
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    $\begingroup$ What OS would you do this on? Do you have access to UNIX tools? Also, please show us the rest of the gene names. What identifiers do you have? The answer will depend on what database the identifiers point to. $\endgroup$ – terdon Dec 24 '14 at 8:09
  • $\begingroup$ @terdon : I have unix tools (debian is the os). OK I will list the genes. $\endgroup$ – dexterdev Dec 24 '14 at 8:18
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    $\begingroup$ It would be quite easy if you have Refseq/ENSEMBL ids for those genes. $\endgroup$ – WYSIWYG Dec 24 '14 at 8:19
  • $\begingroup$ @terdon : I have updated the question. $\endgroup$ – dexterdev Dec 24 '14 at 8:32
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These sequences do not have any standard i.d. The information in Saccharomyces Genome Database is also obsolete (2005) and does not have these identifiers.

These sequences can be found here (in the same site).

Each species has a short name:

ORGANISM        Short Name
S.cerevesiae    Scer
S. bayanus      Sbay
S. paradoxus    Spar
A. gossypii     Agos

.... and so on. 

First letter of genus name in uppercase + first 3 letters of species name in lowercase.

The fasta file (for all ORFs) is:
www.broadinstitute.org/regev/orthogroups/nt/<Shortname>.fasta

From there you can use grep to retrieve the sequence.

So, if you have saved shortnames and gene names two separate files you can do something like this:

for shortname in `cat shortname.txt`; do wget -O tmp.fa "http://www.broadinstitute.org/regev/orthogroups/nt/"$shortname.fasta; grep -A 1 -f ids.txt tmp.fa >> $shortname"_Select.fa"; done
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  • $\begingroup$ OK thankyou, that was really helpful. $\endgroup$ – dexterdev Dec 24 '14 at 11:04
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    $\begingroup$ @dexterdev The searching code can be made better and faster depending on what you really want as output. $\endgroup$ – WYSIWYG Dec 24 '14 at 11:19
  • $\begingroup$ Do you know what is the difference between broadinstitute.org/regev/orthogroups/nt/Scer.fasta and broadinstitute.org/regev/orthogroups/aa/Scer.fasta $\endgroup$ – dexterdev Dec 24 '14 at 11:20
  • $\begingroup$ @dexterdev The first is Nucleotide sequence and second is protein sequence. I gave the first link because you said you wanted nucleotide. $\endgroup$ – WYSIWYG Dec 24 '14 at 11:23
  • $\begingroup$ Sorry for the dumb question. I did looked at it , but did'nt noticed that. Sorry. $\endgroup$ – dexterdev Dec 24 '14 at 11:24
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OK, the first step must be to map all these IDs to the same database. Try using http://uniprot.org if you want protein sequences else, look for each of them and find the corresponding Refseq ID. Since you have IDs from multiple databases, you might need to google them individually. If you know the ID type of each identifier you have, you can use a tool like DAVID's gene name converter to automate it.

Once you have a list of IDs from the same database, save them in a file (one ID per line). Then, for UniProt accessions, you can get the FASTA protein sequence by running:

while read name; do wget -O - http://uniprot.org/$name.fasta; done < names.txt

For RefSeq IDs, you can use the batch retrieval tool of Entrez.

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  • $\begingroup$ Helpful answer. One thing , I am not working on protein sequences, but just nucleotide sequences. $\endgroup$ – dexterdev Dec 24 '14 at 9:33
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    $\begingroup$ When I googled these ids I couldn't find any match in a database. I checked SGD but their repository (from MIT) is obsolete (2005). Even then the orf fasta file (S.paradoxus) did not have an identifier like spar* or SPAR*. Example; first fasta header: ORFN:24882 YPRWsigma4, Contig c301 66351-67256. These are not even from complete assembly; it says contig. $\endgroup$ – WYSIWYG Dec 24 '14 at 10:22

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