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Hi, I can run the code some days ago . But cant run now.  Problem 1: Output is ok ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl) utr5 = getSequence(chromosome=3, start=185514033, end=185535839, type="entrezgene",seqType="5utr", mart=ensembl)  Output :                                                                                                5utr  entrezgene                                                                              Sequence unavailable      10644                                    ...

Sometimes the following function call causes a database exception: > gene.seq <- getSequence (id=gene.map[,"ensembl_transcript_id"], type="ensembl_transcript_id", + seqType="3utr", mart=hmart) I understand the above function must be called by try to capture the eventual error. WHat is not clear to me is how to realize that an error has occurred. The on-line documentation mentions an invisible object of class "try-error". How shall I test whetehr...

Hi !  Facing problem with " getSequence" commend .  when only biomaRt package loaded the following example working well  >mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") >seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptide", mart = mart) show(seq) but when i have loaded the seqinr, i got problem with same commend .  > mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") > seq = getSequence(id="BRCA1", type="hgnc_symbol", seqType="peptid...

...est.fa", rm.dup=F) > aln<-seqaln(aa, exepath="/Users/Fan/Desktop/muscle/src/muscle", file="aa_muscle.fa", protein=T) /Users/Fan/Desktop/muscle/src/musclemuscle -in /var/folders/v9/v95dzKP2E9SAkmd7m4T8dE+++TQ/-Tmp-//RtmpKUJVlZ/file618fb492 -out aa_muscle.fa  -stable -seqtype protein/bin/sh: /Users/Fan/Desktop/muscle/src/musclemuscle: No such file or directory Error in file(file, "r") : cannot open the connection In addition: Warning message: In file(file, "r") :   cannot open file 'aa_muscle.fa': No such file or directory   I have also...

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some

...ST00000377464" [1937] "ENST00000400907" "ENST00000400908" "ENST00000440864" "ENST00000309042" [1941] "ENST00000254325" > genes_seq <- getSequence (id=genes_map[,"ensembl_transcript_id"],type="ensembl_transcript_id", + seqType="3utr",mart=hmart) Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. > tutti i telefonini TIM! [[alternative HTML version deleted]]