Get Started

In this quick guide we will present you the main features of IxoriDB and the output you will get using them:

We will show you how to proceed to explore our database, to find the best homology to your sequences and to interpret the results provided by our webpage.

Browse the database

In order to explore our database you have three main options:

Browse transcript

Only one field is required to make the search, the transcript ID as it is in NCBI or in our transcriptome.

It will lead you to a table with the following information about the browsed transcript:

  1. Transcript ID: ID of the transcript.
  2. Protein ID: ID of the protein with the best homology to the transcript. The protein was selected based on BitScore after a Blast with 4 different databases: ArachnidaDB (local database), SwissProt, Uniref90 and TickSialoFam.
  3. Protein description: Description of the protein with the best homology to the transcript.
  4. Family: Family of the protein with the best homology to the transcript.
  5. GO terms: GO terms associated to the protein or to the conserved domains found in the CDS.
  6. GO terms description: Description of the GO terms.
  7. Interpro domains: Conserved domains existing in the CDS of the transcript. Provided by InterProScan.
  8. Interpro domains description: Description of the conserved domains.
  9. Signal P: Existence of a SignalP in the protein.
  10. Transmembrane domain: Number of transmembrane domains found in the peptide.
  11. Class: According to the classification of our paper, transcripts can encode putatively secreted and annotated proteins, putatively secreted not annotated proteins, putatively non-secreted and annotated proteins and putatively non-secreted not annotated proteins.
  12. Tissue specificity: Indicates if the transcript is midgut specific, salivary gland specific or neutral.
  13. CDS sequence: Nucleotide sequence of the CDS.
  14. Peptide sequence: Peptide sequence of the protein.

This table and every other can be downloaded as excel or tsv files, or even be copied to the clipboard using the buttons in top of it.

According to the expression values (FPKM) found in our study, two interactive graphics will be shown. These graphics can be saved by right clicking on them and choosing “Save image as...”. Also, this graphics are interactive, so they have the following features:

The first table shows how the expression of the transcript varies at different feeding times for the two tissues and the two exposures of the host. This expression value represent the mean of all expression values of the transcript for the samples of that condition.

The second table shows the 88 expression values of the different samples for the transcript. Here you can find the expression values coming for the samples which belong to unfed ticks.

Try it!
Browse protein.

Only one field is required, the protein ID you are looking for as it is in Uniprot or in TickSialoFam.

It will lead you to a table showing all the transcripts which have the best homology with the desired protein. The table have the same fields mentioned in the “Browse transcript” section, but you will find the transcript ID hyperlinked in case you want to see the information and the graphics for an specific transcript as it is explained in the “Browse transcript” section.

This table and every other can be downloaded as excel or tsv files, or even be copied to the clipboard using the buttons in top of it.

Try it!
Browse by feature.

If you want to browse the entire transcriptome you can leave all fields empty and press the search button.

Otherwise you may filter this browse by different features (you can select more than one filter):

  1. Family: Select a family of interest. Only transcript which have the best homology with a protein of that family will be shown.
  2. Secreted: You can browse only transcripts putatively secreted or only transcripts putatively non-secreted.
  3. Transmembrane domain: You can browse only transcripts with at least one transmembrane domain or only transcripts with no transmembrane domain.
  4. Class: You can filter the transcripts that encode proteins of one of the following classes: putatively secreted and annotated proteins, putatively secreted not annotated proteins, putatively non-secreted and annotated proteins and putatively non-secreted not annotated proteins.
  5. Tissue specificity: Only midgut specific transcripts, salivary glands specific transcripts or neutral transcripts will be shown, depending of your choice.
  6. GO terms: Only transcripts with the introduced GO term will be shown.

This search will lead you to a table showing the transcripts that matched your criteria. The table have the same fields as mentioned in the “Browse transcript” section. You will find the transcript ID hyperlinked in case you want to see the information and the graphics for an specific transcript as it is in the “Browse transcript” section.

This table and every other can be downloaded as excel or tsv files, or even be copied to the clipboard using the buttons in top of it.

Try it!

Blast to the database

Using this feature you can blast your sequences to our transcriptome, specifically to the proteins encoded by the coding sequences of the transcript in our transcriptome.

You can paste a sequence in Fasta format. Or select a Fasta file from your computer.

You need to select the type of sequence introduced: Peptide or nucleotide. Then, you can just press the button to find the transcripts with the best homology to your sequences.

There is a section with advanced blast options, just in case you want to customize the alignment:

  1. E-value cut-off: Maximum e-value for the alignment to be considered as valid.
  2. Word-size: Length of an exact sequence match, as start region for the final alignment.
  3. Max targets per seq: Number of hits shown per sequence.

Once the blast is finished, the output of the blast will be shown in a table that can be copied to the clipboard or downloaded in excel or tsv format. The table will have the following fields:

  1. Query ID: The name of your sequence.
  2. Hit ID: The ID of the transcript of our database. It is hyperlinked in case you want to see the information and the graphics for an specific transcript as it is explained in the “Browse transcript” section.
  3. Identity: Percentage of identical matches.
  4. Length: Alignment length or sequence overlap.
  5. Mismatch: Number of mismatches.
  6. Gap openings: Number of gap openings.
  7. Query start: Start of alignment in query.
  8. Query end: End of alignment in query.
  9. Hit start: Start of alignment in hit.
  10. Hit end: End of alignment in hit.
  11. Expect value: E-value (number of expected hits of similar quality that could be found just by chance).
  12. Bit Score: The required size of a sequence database in which the current match could be found just by chance.

You can find more information about the E-value and Bit Score here.

Try it!

Get Annotation

This tool allows you to get the annotation (family, GO terms, Putative secretion...) of set of transcripts determined by the user.

This tool need a comma separated list of transcript IDs. Transcript IDs can be obtained from the tables that every feature of this webpage provide you or from any of the downloadable files in the Downloads section.

The annotation of the set of transcript will be shown in a table that can be copied to the clipboard or downloaded in excel or tsv format. The table have the following fields:

  1. Transcript ID: ID of the transcript.
  2. Protein ID: ID of the protein with the best homology to the transcript. The protein was selected based on BitScore after a Blast with 4 different databases: ArachnidaDB (local database), SwissProt, Uniref90 and TickSialoFam.
  3. Protein description: Description of the protein with the best homology to the transcript.
  4. Family: Family of the protein with the best homology to the transcript.
  5. GO terms: GO terms associated to the protein or to the conserved domains found in the CDS.
  6. GO terms description: Description of the GO terms.
  7. Interpro domains: Conserved domains existing in the CDS of the transcript. Provided by InterProScan.
  8. Interpro domains description: Description of the conserved domains.
  9. Signal P: Existence of a SignalP in the protein.
  10. Class: According to the classification of our paper, transcripts can encode putatively secreted and annotated proteins, putatively secreted not annotated proteins, putatively non-secreted and annotated proteins and putatively non-secreted not annotated proteins.
Try it!