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So, if this is the first file, save the first field of each line (the gene name) in the array wantedGenes. if($3=="gene"){ : if this line is a 'gene' entry. gsub(/";*/,"",$10); : the gene names in the … 10th field (the gene name), the 4th (start) and the 5th field (end). …

GFF2PS was developed for exactly this sort of thing. It takes a GFF file as input, and will produce a pretty PS output showing the annotations. It was used to create the poster for Celera's human geno …

There's an app for that! The exonerate package (see here) includes a nice fastaexplode command that does exactly what you're looking for and will be much, much faster than anything we give you here si …

If you want to use the gene name (2nd and 4th fields, in your example), just run: awk 'print $2,$4' netw.txt > netw.gr If you want to use the Entrez geneIDs instead, run: awk 'print $1,$3' netw.txt … > netw.gr Then, as others already mentioned, install Cytoscape, launch it and import your gene list: In the welcome screen, select "From Network File …

Click on "Filters", and set Gene type to coding and Transcript type to protein_coding. From "Attributes", select whatever you want to see. The "CDS Length" is under "Structures". …

Many interaction databases now work with PSI format files. Most of the main databases can do this and the EBI has set up PSICQUIC View, a very useful page where you can query multiple databases at onc …

a numerical gene ID. … Some of them may graduate to a full gene name, others might not. As for uniqueness, no absolutely not. GenBank gene IDs are unique, they don't imply homology. Only one gene can have a given ID. …

For example, this is the exonic structure shown for ENST00000617185, one of the transcripts of the human P53 gene: The boxes are exons and the lines are introns. …

Search for your gene of interest, choose your transcript, go to the page of its protein product(s), and select "Domains & Features" from the right-hand menu (using human p53 as an example): Domain source …

Paralogs are duplicates by definition, and whether a gene is a pseudogene or still active has no bearing on whether it comes from a duplication. … Are the protein domains of the gene products conserved? Is the exonic structure of the gene conserved? …

You don't want BLAST here, or at least not regular BLASTn. A better method would be to use tBLASTn to map the known C. Elegans proteins to the translated genome. However, I would recommend using a sli …

If your file doesn't contain the rsIDs, you can use a tool like Ensembl's VEP to annotate the file and get rsIDs as well. Of course, not all variants have an rsID so don't expect to find one for every …